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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/hyphy">Debian Med / hyphy</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/e5c8fd32984d059ec09233aa8f7e5cdb888c538c">e5c8fd32</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-21T13:35:05+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.5.24+dfsg</pre>
</li>
</ul>
<h4>15 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#4ed0809c2483f5150cdfd2c3bf07d212387406d0">
res/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf
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<li class="file-stats">
<a href="#80cb7c212661a2afbd05c16dce9f84f45709578e">
res/TemplateBatchFiles/SelectionAnalyses/PRIME.bf
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<li class="file-stats">
<a href="#48abec8e0d198814ad3898dd7c82ef8b52eef776">
res/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf
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<li class="file-stats">
<a href="#07aceb8d215a75908cea626d9c80bc2a7c06639c">
src/core/global_things.cpp
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<li class="file-stats">
<a href="#d01e581f215a0108a96d0f6d1b081d43c2e0a8a3">
src/core/include/defines.h
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<li class="file-stats">
<a href="#7277ab70f1a79733638d6141d1cb1d3f8b9c26c2">
src/core/include/likefunc.h
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<li class="file-stats">
<a href="#2a8dd324ded753b0b3c559ac3950a2881ccd7a93">
src/core/likefunc.cpp
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<li class="file-stats">
<a href="#81843dd3cf849d08e0f197d837dd373534c7c756">
src/core/matrix.cpp
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<li class="file-stats">
<a href="#9f127084157a2a4e11faf03320db0541dbae15dc">
src/core/tree_evaluator.cpp
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<li class="file-stats">
<a href="#4ca2d78a3895acfaccf8d26bda9d0ec8aefb2c65">
src/lib/setup.py
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<li class="file-stats">
<a href="#adf5ba83265c3f16b63f5fab29404568aa294038">
tests/hbltests/Results/HIVSweden.out
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<li class="file-stats">
<a href="#3bbc19efb5ab1243a9d0c4627a24ef88cf1f3ca0">
tests/hbltests/Results/HIVSweden.out_MODEL_-1.nex
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<li class="file-stats">
<a href="#96e4cef3847de919b0f245e8443e6befe26c217b">
tests/hbltests/Results/HIVSweden.out_MODEL_0.nex
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<li class="file-stats">
<a href="#dc4367ca74d002d80f8b7061c05e7d0232904a74">
tests/hbltests/Results/HIVSweden.out_MODEL_1.nex
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</li>
</ul>
<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/e5c8fd32984d059ec09233aa8f7e5cdb888c538c#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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1
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<td class="diff-line-num new_line" 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">
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">cmake_minimum_required</span><span class="p">(</span>VERSION 3.12<span class="p">)</span></span>
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<td class="diff-line-num old_line" 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="diff-line-num new_line" 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="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span>HyPhy<span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">cmake_policy</span><span class="p">(</span>VERSION 3.0.0<span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4
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<td class="diff-line-num new_line old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#cmake_policy(SET CMP0026 OLD)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
5
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<td class="diff-line-num new_line old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC5" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#cmake_policy(SET CMP0004 OLD)</span></span>
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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="cmake"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">enable_testing</span><span class="p">()</span></span>
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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="cmake"></span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<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 +12,7 @@ set(CMAKE_CONFIGURATION_TYPES Release)</td>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
14
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cmake"></span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
15
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>NOAVX OFF<span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
16
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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>NOSSE3 OFF<span class="p">)</span></span>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>NONEON OFF<span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
17
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cmake"></span>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#-------------------------------------------------------------------------------</span></span>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># SSE MACROS</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="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">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,6 +43,34 @@ macro(PCL_CHECK_FOR_SSE3)</td>
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44
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<td class="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cmake"> HAVE_SSE3_EXTENSIONS<span class="p">)</span></span>
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<td class="diff-line-num 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">
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<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endmacro</span><span class="p">(</span>PCL_CHECK_FOR_SSE3<span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#-------------------------------------------------------------------------------</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># NEON MACROS</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#-------------------------------------------------------------------------------</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cmake"></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">macro</span><span class="p">(</span>PCL_CHECK_FOR_NEON<span class="p">)</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">include</span><span class="p">(</span>CheckCXXSourceRuns<span class="p">)</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_REQUIRED_FLAGS<span class="p">)</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cmake"></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;">#if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_REQUIRED_FLAGS <span class="s2" style="color: #d14;">"-msse3"</span><span class="p">)</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;">#endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cmake"></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">check_cxx_source_runs</span><span class="p">(</span><span class="s2" style="color: #d14;">"</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cmake"><span class="s2" style="color: #d14;"> #include <stdio.h></span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cmake"><span class="s2" style="color: #d14;"> #include <arm_neon.h></span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cmake"><span class="s2" style="color: #d14;"> int main() {</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cmake"><span class="s2" style="color: #d14;"> double array[4] = {4.,2.,3.,4};</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cmake"><span class="s2" style="color: #d14;"> float64x2_t a1 = vld1q_f64 (array),</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cmake"><span class="s2" style="color: #d14;"> a2 = vld1q_f64 (array+2);</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cmake"><span class="s2" style="color: #d14;"> a1 = vmulq_f64 (a1,a2);</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cmake"><span class="s2" style="color: #d14;"> vst1q_lane_f64 (array, a1, 0);</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cmake"><span class="s2" style="color: #d14;"> printf (</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">%g</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">, array[0]);</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cmake"><span class="s2" style="color: #d14;"> return 0;</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cmake"><span class="s2" style="color: #d14;"> }"</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cmake"> HAVE_NEON_EXTENSIONS<span class="p">)</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endmacro</span><span class="p">(</span>PCL_CHECK_FOR_NEON<span class="p">)</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cmake"></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cmake"></span>
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47
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#-------------------------------------------------------------------------------</span></span>
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48
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># SSE MACROS</span></span>
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49
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cmake"><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="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -219,6 +246,13 @@ if (CMAKE_CXX_COMPILER_ID MATCHES "Clang")</td>
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219
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246
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">HAVE_SSE3_EXTENSIONS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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220
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<td class="diff-line-num new_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span> <span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">HAVE_AVX_EXTENSIONS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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221
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248
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span>NOAVX<span class="p">)</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cmake"> </span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>NOT NONEON<span class="p">)</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">PCL_CHECK_FOR_NEON</span><span class="p">()</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">HAVE_NEON_EXTENSIONS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_definitions</span> <span class="p">(</span>-D_SLKP_USE_ARM_NEON<span class="p">)</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">HAVE_NEON_EXTENSIONS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span>NOT NONEON<span class="p">)</span></span>
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222
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cmake"></span>
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223
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<td class="diff-line-num new_line" 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">
257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set_property</span><span class="p">(</span></span>
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224
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="cmake"> SOURCE <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">SRC_CORE</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">SRC_NEW</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">SRC_UTILS</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">SRC_UNIXMAIN</span><span class="si" style="color: #d14;">}</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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -503,11 +537,13 @@ set_target_properties(</td>
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503
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537
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="cmake"> HYPHYDEBUG</span>
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504
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538
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="cmake"> PROPERTIES</span>
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505
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">OPENMP_FOUND</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="cmake"> COMPILE_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">DEFAULT_COMPILE_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">DEFAULT_DEBUG_WARNING_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">OpenMP_CXX_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">MPI_COMPILE_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -g -fprofile-arcs -ftest-coverage -fsanitize=address -fsanitize=leak -O0 "</span></span>
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="cmake"> LINK_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">DEFAULT_COMPILE_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">OpenMP_CXX_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">MPI_LINK_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -g -fprofile-arcs -ftest-coverage -fsanitize=address -O0 "</span></span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;">#COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} ${OpenMP_CXX_FLAGS} ${MPI_COMPILE_FLAGS} -g -fsanitize=address -fsanitize=leak -O0 "</span></span>
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="cmake"> COMPILE_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">DEFAULT_COMPILE_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">DEFAULT_DEBUG_WARNING_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">OpenMP_CXX_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">MPI_COMPILE_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -g -fsanitize=address -O0 "</span></span>
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="cmake"> LINK_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">DEFAULT_COMPILE_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">OpenMP_CXX_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">MPI_LINK_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -g -fsanitize=address -O0 "</span></span>
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">else</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">OPENMP_FOUND</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="cmake"> COMPILE_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">DEFAULT_COMPILE_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">DEFAULT_DEBUG_WARNING_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -g -fprofile-arcs -ftest-coverage -fsanitize=address -fsanitize=leak -O0 "</span></span>
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="cmake"> LINK_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">DEFAULT_COMPILE_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -g -fprofile-arcs -ftest-coverage -fsanitize=address -O0 "</span></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;">#COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} -g -fsanitize=address -fsanitize=leak -O0 "</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="cmake"> COMPILE_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">DEFAULT_COMPILE_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">DEFAULT_DEBUG_WARNING_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -g -fsanitize=address -O0 "</span></span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="cmake"> LINK_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">DEFAULT_COMPILE_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -g -fsanitize=address -O0 "</span></span>
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">OPENMP_FOUND</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="cmake"><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC549" class="line" lang="cmake"></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/e5c8fd32984d059ec09233aa8f7e5cdb888c538c#4ed0809c2483f5150cdfd2c3bf07d212387406d0"><strong>res/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -429,34 +429,42 @@ if (busted.do_srv_hmm) {</td>
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<pre style="margin: 0;"> <span id="LC429" 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 (((busted</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bsrel_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;">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;">rate_variation</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">hmm_lambda</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</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;">6"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "");</span></span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">DeclareGlobalWithRanges ("busted</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;">scaler"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 1000);</span></span>
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">busted</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">grid_search</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">results = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">FitLF (busted</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;"> busted</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;"> busted</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;"> busted</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">final_partitioned_mg_results</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> busted</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;"> {</span></span>
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "retain</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;">object": TRUE</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 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;">proportional_branch_length_scaler : </span></span>
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"0" : "busted</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;">scaler"}</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">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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<pre style="margin: 0;">+<span id="LC433" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (Type (debug</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">checkpoint) != "String") {</span></span>
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<pre style="margin: 0;">+<span id="LC435" 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;">DeclareGlobalWithRanges ("busted</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;">scaler"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 1000);</span></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> busted</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">grid_search</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">results = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">FitLF (busted</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;"> busted</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;"> busted</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;"> busted</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">final_partitioned_mg_results</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> busted</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;"> {</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "retain</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;">object": TRUE</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 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;">proportional_branch_length_scaler : </span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"0" : "busted</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;">scaler"}</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 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;">optimization_settings : </span></span>
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "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>
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "MAXIMUM_OPTIMIZATION_ITERATIONS" : 500</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "OPTIMIZATION_PRECISION" : busted</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">nm</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">precision</span></span>
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } </span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>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;">optimization_settings : </span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>{</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>"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>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>"MAXIMUM_OPTIMIZATION_ITERATIONS" : 500</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>"OPTIMIZATION_PRECISION" : busted</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">nm</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">precision</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>} </span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<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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<pre style="margin: 0;">-<span id="LC446" 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;">search_grid : busted</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">initial_grid</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC447" 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;">search_restarts : busted</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;">initial_guesses</span></span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">});</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">search_grid : busted</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">initial_grid</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">search_restarts : busted</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;">initial_guesses</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"> </span>});</span></span>
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">busted</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">full_model = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">FitLF (busted</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;"> busted</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;"> busted</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;"> busted</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">grid_search</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;"> busted</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;"> {</span></span>
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "retain</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;">object": TRUE</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 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;">optimization_settings : </span></span>
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "OPTIMIZATION_METHOD" : "hybrid"</span></span>
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<pre style="margin: 0;">-<span id="LC456" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } </span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> busted</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">full_model = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">FitLF (busted</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;"> busted</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;"> busted</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;"> busted</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">grid_search</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;"> busted</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;"> {</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "retain</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;">object": TRUE</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 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;">optimization_settings : </span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "OPTIMIZATION_METHOD" : "hybrid"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //"OPTIMIZATION_PRECISION" : 1</span><span class="nf" style="color: #900; font-weight: 600;">.</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } </span></span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> });</span></span>
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> });</span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">} else {</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ExecuteAFile (debug</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">checkpoint);</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> GetString (lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> LikelihoodFunction</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0);</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> busted</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">full_model = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ExtractMLEs (lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> busted</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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<pre style="margin: 0;">+<span id="LC466" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> busted</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">full_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;">likelihood_function</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = lf;</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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<pre style="margin: 0;"> <span id="LC470" 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 BUSTED 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -464,6 +472,7 @@ io.SpoolLFToPath(busted.full_model[terms.likelihood_function], io.PromptUserForF</td>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC473" 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("BUSTED"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "main"</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 (busted</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">full_model</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;"> busted</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>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">//VERBOSITY_LEVEL = 101;</span></span>
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<pre style="margin: 0;"> <span id="LC478" 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("BUSTED"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "main"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "* For *test* branches</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> the following rate distribution for branch</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">site combinations was inferred");</span></span>
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<li id="80cb7c212661a2afbd05c16dce9f84f45709578e">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/e5c8fd32984d059ec09233aa8f7e5cdb888c538c#80cb7c212661a2afbd05c16dce9f84f45709578e"><strong>res/TemplateBatchFiles/SelectionAnalyses/PRIME.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">@@ -21,6 +21,9 @@ LoadFunctionLibrary("modules/io_functions.ibf");</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">LoadFunctionLibrary("modules/selection_lib</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ibf");</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC27" 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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<pre style="margin: 0;"> <span id="LC28" 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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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Display analysis information</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -103,7 +106,11 @@ This table is meant for HTML rendering in the results web-app; can use HTML char</td>
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103
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">is 'pop</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">over' explanation of terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> This is ONLY saved to the JSON file</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> For Markdown screen output see</span></span>
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104
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">the next set of variables</span><span class="nf" style="color: #900; font-weight: 600;">.</span></span>
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105
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">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>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">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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<pre style="margin: 0;">+<span id="LC111" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="brainfuck"></span>
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113
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<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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107
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114
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<pre style="margin: 0;"> <span id="LC114" 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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108
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 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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109
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 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="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -112,9 +119,10 @@ prime.table_output_options = { terms.table_options.header : TRUE,</td>
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112
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "1" : 12</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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113
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "2" : 12</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "3" : 12</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "4" : <span class="idiff left right">5</span>0</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<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">4</span>0</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC123" 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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<pre style="margin: 0;">-<span id="LC117" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "6" : 12}</span></span>
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<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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<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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<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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<pre style="margin: 0;"> <span id="LC127" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="brainfuck"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -129,6 +137,7 @@ prime.property_set = io.SelectAnOption (</td>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Atchley":"Use the five properties derived from a factor analysis of 500 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 class="p">[</span><span class="c1" style="color: #998; font-style: italic;">Table 2 in PNAS (2005) 102(18) 6395</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">6400 doi: 10</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">1073/pnas</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">0408677102</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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<pre style="margin: 0;"> <span id="LC139" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "LCAP":"Use the five properties defined in the Conant and Stadler LCAP model </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">Mol Biol Evol (2009) 26 (5): 1155</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1161</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;">1093/molbev/msp031</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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<pre style="margin: 0;">+<span id="LC140" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Random" : "Random properties (for null hypothesis testing)"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Custom":"Load the set of properties from a file"</span></span>
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<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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<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 match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -155,6 +164,7 @@ for (_partition_, _selection_; in; prime.selected_branches) {</td>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC166" 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;">pairwise_counts = genetic_code</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ComputePairwiseDifferencesAndExpectedSites(prime</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;">code</span><span class="p">]</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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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon_table = genetic_code</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">DefineCodonToAAMapping (prime</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;">code</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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158
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="brainfuck"></span>
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159
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">selection</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">startTimer (prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">timers</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Model fitting"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">1);</span></span>
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160
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="brainfuck"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -296,6 +306,9 @@ prime.lambda_range = {</td>
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296
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306
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<pre style="margin: 0;"> <span id="LC306" 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: "15"</span></span>
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297
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> };</span></span>
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298
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="brainfuck"></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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299
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312
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<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 = { 6 </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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300
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313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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301
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314
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<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="diff-line-num unfold js-unfold old_line" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); 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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -375,7 +388,8 @@ prime.report.significant_site = {{"" + (1+((prime.filter_specification[prime.rep</td>
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375
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 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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376
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 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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377
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390
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<pre style="margin: 0;"> <span id="LC390" 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;">rate_to_screen ( 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;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report_rate)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> // property importance </span></span>
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<td class="diff-line-num old old_line" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
378
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<pre style="margin: 0;">-<span id="LC378" 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;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">print_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;">7</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3) // property p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">value </span></span>
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 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;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">print_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;">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;"> // property p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">value </span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="brainfuck"><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;"> 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 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;">property_report_name</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span></span>
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379
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}};</span></span>
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380
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394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="brainfuck"></span>
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="brainfuck"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -659,6 +673,9 @@ lfunction prime.handle_a_site (lf_fel, lf_prop, filter_data, partition_index, pa</td>
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659
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673
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<pre style="margin: 0;"> <span id="LC673" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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674
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<pre style="margin: 0;"> <span id="LC674" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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675
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<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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<pre style="margin: 0;">+<span id="LC676" 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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677
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<pre style="margin: 0;">+<span id="LC677" 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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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> DeleteObject (ancestral_info);</span></span>
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679
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<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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663
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680
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<pre style="margin: 0;"> <span id="LC680" 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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664
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681
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<pre style="margin: 0;"> <span id="LC681" 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="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -691,6 +708,7 @@ lfunction prime.handle_a_site (lf_fel, lf_prop, filter_data, partition_index, pa</td>
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691
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708
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<pre style="margin: 0;"> <span id="LC708" 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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692
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709
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<pre style="margin: 0;"> <span id="LC709" 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>
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693
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710
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<pre style="margin: 0;"> <span id="LC710" 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>
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<pre style="margin: 0;">+<span id="LC711" 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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<pre style="margin: 0;"> <span id="LC712" 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>
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713
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<pre style="margin: 0;"> <span id="LC713" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> };</span></span>
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<pre style="margin: 0;"> <span id="LC714" 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">@@ -738,6 +756,71 @@ function prime.report.echo (prime.report.site, prime.report.partition, prime.rep</td>
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756
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<pre style="margin: 0;"> <span id="LC756" class="line" lang="brainfuck"></span>
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757
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<pre style="margin: 0;"> <span id="LC757" 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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758
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<pre style="margin: 0;"> <span id="LC758" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 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>
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (None != sub_profile) {</span></span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> total_sub_count = 0;</span></span>
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="brainfuck"></span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sub_by_count = {"Overall" : {}};</span></span>
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 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>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 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>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="brainfuck"></span>
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775
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<pre style="margin: 0;">+<span id="LC775" 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>
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776
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<pre style="margin: 0;">+<span id="LC776" 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>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> c = Abs (b);</span></span>
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778
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<pre style="margin: 0;">+<span id="LC778" 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>
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779
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<pre style="margin: 0;">+<span id="LC779" 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>
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780
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<pre style="margin: 0;">+<span id="LC780" 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>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (Abs (ai) == 0) {ai = "?";}</span></span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (Abs (aj) == 0) {aj = "?";}</span></span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="brainfuck"></span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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785
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<pre style="margin: 0;">+<span id="LC785" 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;"> counts; in; sub_by_count) { </span></span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if ((counts/c)==0) {</span></span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> counts </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">c</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = {};</span></span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> delta = "";</span></span>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (p != "Overall") {</span></span>
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792
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<pre style="margin: 0;">+<span id="LC792" 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;">Format (Abs (((^"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="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 class="p">[</span><span class="c1" style="color: #998; font-style: italic;">ai</span><span class="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;">properties")</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 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;">)</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;">2) </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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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (ai != aj) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> counts</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">c</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;"> (((^"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 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;"> (^"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 class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> delta);</span></span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> counts</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">c</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;"> ai;</span></span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="brainfuck"></span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sub_profile = {};</span></span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (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>
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806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="brainfuck"></span>
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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sorted_subs = {Abs (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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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> j = 0;</span></span>
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809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (i</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> v; in; count) {</span></span>
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810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sorted_subs</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 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;">i);</span></span>
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811
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> j </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1; </span></span>
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812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sub_profile1 = {};</span></span>
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814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (i; in; sorted_subs % 0) {</span></span>
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815
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sub_profile1 </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> ("</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">" </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;">i) </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">" </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;">count </span><span class="p">[</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">));</span></span>
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sub_profile </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;"> = sub_profile1;</span></span>
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC820" 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" = sub_profile;</span></span>
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC824" 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>
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<pre style="margin: 0;"> <span id="LC825" 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>
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<pre style="margin: 0;"> <span id="LC826" class="line" lang="brainfuck"></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/e5c8fd32984d059ec09233aa8f7e5cdb888c538c#48abec8e0d198814ad3898dd7c82ef8b52eef776"><strong>res/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -666,12 +666,34 @@ function fel.apply_proportional_site_constraint (tree_name, node_name, alpha_par</td>
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">//</span><span class="nf" style="color: #900; font-weight: 600;">----------------------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">handle_a_site (lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> filter_data</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;"> pattern_info</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;"> branch_sets</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> parameter_names</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> permutation) {</span></span>
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC669" 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;">Keys (branch_sets)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_node_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> lengths_by_class = {};</span></span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (_node_; in; utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Keys (branch_sets)) {</span></span>
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _node_class_ = branch_sets</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _beta_scaler = parameter_names</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_class_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> lengths_by_class</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_class_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">apply_proportional_site_constraint ("fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_tree"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _node_</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _beta_scaler</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (( (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">final_partitioned_mg_results")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">); </span></span>
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC679" 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;">Keys (branch_sets)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_node_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC680" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> '_node_class_ = (`&branch_sets`)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;"> <span id="LC681" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _beta_scaler = (`¶meter_names`)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_class_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;"> <span id="LC682" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">apply_proportional_site_constraint ("fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_tree"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _node_</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _beta_scaler</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC683" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (( fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">final_partitioned_mg_results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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<pre style="margin: 0;">-<span id="LC674" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ');</span></span>
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ');*/</span></span>
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ignorable = {};</span></span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">t; in; utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Values (branch_sets)) {</span></span>
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if ( lengths_by_class</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">t</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> == 0) {</span></span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ignorable </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">parameter_names</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">t</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;"> = 1;</span></span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ignorable </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">parameter_names</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">t</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;"> = 0;</span></span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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695
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<pre style="margin: 0;">+<span id="LC695" 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 (lengths_by_class);</span></span>
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696
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<pre style="margin: 0;">+<span id="LC696" 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 (ignorable);</span></span>
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697
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<pre style="margin: 0;"> <span id="LC697" class="line" lang="brainfuck"></span>
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698
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<pre style="margin: 0;"> <span id="LC698" 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</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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677
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699
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<pre style="margin: 0;"> <span id="LC699" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ExecuteCommands (filter_data);</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">@@ -765,13 +787,15 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod</td>
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787
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<pre style="margin: 0;"> <span id="LC787" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ^ref_parameter = sum /denominator;</span></span>
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789
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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792
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<pre style="margin: 0;"> <span id="LC792" class="line" lang="brainfuck"></span>
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769
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793
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<pre style="margin: 0;"> <span id="LC793" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (testable == 1) {</span></span>
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770
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794
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<pre style="margin: 0;"> <span id="LC794" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetConstraint ((^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler_parameter_names")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">tree_attributes</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">background"</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">ref_parameter</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "");</span></span>
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<pre style="margin: 0;"> <span id="LC795" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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772
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796
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<pre style="margin: 0;"> <span id="LC796" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (_gname_; in; ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branches</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">testable") {</span></span>
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797
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<pre style="margin: 0;"> <span id="LC797" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _pname_ = (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler_parameter_names")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_gname_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">-<span id="LC774" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (_pname_ != ref_parameter && (<span class="idiff left">^"fel</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">ignorable"</span>)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_pname_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> == 0) {</span></span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (_pname_ != ref_parameter && (<span class="idiff left right">ignorable</span>)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_pname_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> == 0) {</span></span>
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<pre style="margin: 0;"> <span id="LC799" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetConstraint (_pname_</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">ref_parameter</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "");</span></span>
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800
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<pre style="margin: 0;"> <span id="LC800" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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801
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<pre style="margin: 0;"> <span id="LC801" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="812" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -788,8 +812,9 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod</td>
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788
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812
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<pre style="margin: 0;"> <span id="LC812" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> v1n = (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branches</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">testable")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">v</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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789
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813
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<pre style="margin: 0;"> <span id="LC813" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> v2n = (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branches</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">testable")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">v2</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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790
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814
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<pre style="margin: 0;"> <span id="LC814" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">RestoreLFStateFromSnapshot (lf_id</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> snapshot);</span></span>
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815
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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816
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<pre style="margin: 0;"> <span id="LC816" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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792
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<pre style="margin: 0;">-<span id="LC792" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if ((<span class="idiff left">^"fel</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">ignorable")</span></span><span class="p"><span class="idiff">[</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">(^"fel</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">scaler_parameter_names")</span></span><span class="p"><span class="idiff">[</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">v1n</span></span><span class="p"><span class="idiff">]]</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff"> || (^"fel</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">ignorable"</span>)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">(^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler_parameter_names")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">v2n</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;">) {</span></span>
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817
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if ((<span class="idiff left">ignorable)</span></span><span class="p"><span class="idiff">[</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">(^"fel</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">scaler_parameter_names")</span></span><span class="p"><span class="idiff">[</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">v1n</span></span><span class="p"><span class="idiff">]]</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"> || (ignorable</span>)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">(^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler_parameter_names")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">v2n</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;">) {</span></span>
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793
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818
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<pre style="margin: 0;"> <span id="LC818" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //console</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log (v1n </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "|" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> v2n </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> " is ignorable");</span></span>
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794
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819
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<pre style="margin: 0;"> <span id="LC819" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (pairwise</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">v1n </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "|" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> v2n</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) = alternative;</span></span>
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820
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<pre style="margin: 0;"> <span id="LC820" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else { </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">@@ -811,6 +836,9 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod</td>
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811
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<pre style="margin: 0;"> <span id="LC836" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> p_values = {};</span></span>
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812
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<pre style="margin: 0;"> <span id="LC837" 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;">"overall"</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;">^'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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813
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838
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<pre style="margin: 0;"> <span id="LC838" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> test_keys = {};</span></span>
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">RestoreLFStateFromSnapshot (lf_id</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> snapshot);</span></span>
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="brainfuck"></span>
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842
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<pre style="margin: 0;"> <span id="LC842" class="line" lang="brainfuck"></span>
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843
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<pre style="margin: 0;"> <span id="LC843" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (^'fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test_count' </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;"> 1) {</span></span>
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816
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844
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<pre style="margin: 0;"> <span id="LC844" class="line" lang="brainfuck"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -826,7 +854,6 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod</td>
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854
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<pre style="margin: 0;"> <span id="LC854" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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827
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855
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<pre style="margin: 0;"> <span id="LC855" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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828
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856
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<pre style="margin: 0;"> <span id="LC856" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC829" class="line" lang="brainfuck"></span>
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857
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<pre style="margin: 0;"> <span id="LC857" 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>
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831
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858
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<pre style="margin: 0;"> <span id="LC858" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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832
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859
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<pre style="margin: 0;"> <span id="LC859" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (permutation == FALSE && (Min (p_values</span><span class="nf" style="color: #900; font-weight: 600;">,</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;">"value"</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;">= ^'fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p_value') {</span></span>
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<li id="07aceb8d215a75908cea626d9c80bc2a7c06639c">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/e5c8fd32984d059ec09233aa8f7e5cdb888c538c#07aceb8d215a75908cea626d9c80bc2a7c06639c"><strong>src/core/global_things.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -121,7 +121,7 @@ namespace hy_global {</td>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">kErrorStringDatasetRefIndexError</span> <span class="p">(</span><span class="s" style="color: #d14;">"Dataset index reference out of range"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">kErrorStringMatrixExportError</span> <span class="p">(</span><span class="s" style="color: #d14;">"Export matrix called with a non-polynomial matrix argument"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">kErrorStringNullOperand</span> <span class="p">(</span><span class="s" style="color: #d14;">"Attempting to operate on an undefined value; this is probably the result of an earlier 'soft' error condition"</span><span class="p">),</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">kHyPhyVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"2.5.2<span class="idiff left right">3</span>"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">kHyPhyVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"2.5.2<span class="idiff left right">4</span>"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"> <span class="n" style="color: #333;">kNoneToken</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"None"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">kNullToken</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"null"</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/e5c8fd32984d059ec09233aa8f7e5cdb888c538c#d01e581f215a0108a96d0f6d1b081d43c2e0a8a3"><strong>src/core/include/defines.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">@@ -336,9 +336,15 @@ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.</td>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//TODO 20170413: not sure where to put the conditional includes below</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_ARM_NEON</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#include <arm_neon.h></span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_SSE_INTRINSICS</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <pmmintrin.h></span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//#include "sse2neon.h"</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//#else</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#include <pmmintrin.h></span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//#endif</span></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_AVX_INTRINSICS</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/e5c8fd32984d059ec09233aa8f7e5cdb888c538c#7277ab70f1a79733638d6141d1cb1d3f8b9c26c2"><strong>src/core/include/likefunc.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">@@ -614,7 +614,8 @@ protected:</td>
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC615" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">smoothingTerm</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC616" class="line" lang="cpp"> <span class="n" style="color: #333;">smoothingReduction</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC617" class="line" lang="cpp"> <span class="n" style="color: #333;">smoothingPenalty</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="cpp"> <span class="n" style="color: #333;">smoothingPenalty</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="cpp"> <span class="n" style="color: #333;">errorTolerance</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC619" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_LFENGINE_REWRITE_</span></span>
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<pre style="margin: 0;"> <span id="LC621" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/e5c8fd32984d059ec09233aa8f7e5cdb888c538c#2a8dd324ded753b0b3c559ac3950a2881ccd7a93"><strong>src/core/likefunc.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -559,8 +559,7 @@ _LikelihoodFunction::_LikelihoodFunction (void) {</td>
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_______________________________________________________________________________________</span></span>
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">_LikelihoodFunction</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Init</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">_LikelihoodFunction</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Init</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="cpp"> <span class="n" style="color: #333;">siteResults</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nil</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="cpp"> <span class="n" style="color: #333;">bySiteResults</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nil</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="cpp"> <span class="n" style="color: #333;">hasBeenSetUp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -571,6 +570,7 @@ void _LikelihoodFunction::Init (void)</td>
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="cpp"> <span class="n" style="color: #333;">evalsSinceLastSetup</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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571
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="cpp"> <span class="n" style="color: #333;">siteArrayPopulated</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="cpp"> <span class="n" style="color: #333;">smoothingTerm</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="cpp"> <span class="n" style="color: #333;">errorTolerance</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="cpp"> <span class="n" style="color: #333;">smoothingPenalty</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="cpp"> <span class="n" style="color: #333;">conditionalInternalNodeLikelihoodCaches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nil</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3638,7 +3638,8 @@ void _LikelihoodFunction::SetupLFCaches (void) {</td>
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3638
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<pre style="margin: 0;"> <span id="LC3638" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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3639
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3639
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<pre style="margin: 0;"> <span id="LC3639" class="line" lang="cpp"></span>
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3640
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3640
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<pre style="margin: 0;"> <span id="LC3640" class="line" lang="cpp"> <span class="n" style="color: #333;">evalsSinceLastSetup</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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3641
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<pre style="margin: 0;">-<span id="LC3641" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC3641" 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;">maxFilterSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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3642
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<pre style="margin: 0;">+<span id="LC3642" class="line" lang="cpp"> </span>
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3643
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<pre style="margin: 0;"> <span id="LC3643" 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;">theTrees</span><span class="p">.</span><span class="n" style="color: #333;">lLength</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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3644
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<pre style="margin: 0;"> <span id="LC3644" class="line" lang="cpp"> <span class="n" style="color: #333;">_TheTree</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetIthTree</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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3645
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<pre style="margin: 0;"> <span id="LC3645" class="line" lang="cpp"> <span class="n" style="color: #333;">_DataSetFilter</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">theFilter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetIthFilter</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3663,6 +3664,7 @@ void _LikelihoodFunction::SetupLFCaches (void) {</td>
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3663
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<pre style="margin: 0;"> <span id="LC3664" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC3665" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">ambig_resolution_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1L</span><span class="p">;</span></span>
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3665
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3666
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<pre style="margin: 0;"> <span id="LC3666" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC3667" class="line" lang="cpp"> <span class="n" style="color: #333;">maxFilterSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAX</span> <span class="p">(</span><span class="n" style="color: #333;">maxFilterSize</span><span class="p">,</span> <span class="n" style="color: #333;">theFilter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetSiteCountInUnits</span><span class="p">());</span></span>
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3666
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3668
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<pre style="margin: 0;"> <span id="LC3668" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">leafCount</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1UL</span><span class="p">)</span> <span class="p">{</span></span>
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3667
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3669
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<pre style="margin: 0;"> <span id="LC3669" class="line" lang="cpp"> <span class="n" style="color: #333;">conditionalInternalNodeLikelihoodCaches</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="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;">MemAllocate</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;">patternCount</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">stateSpaceDim</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">iNodeCount</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cT</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">categoryCount</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="mi" style="color: #099;">64</span><span class="p">);</span></span>
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3668
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3670
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<pre style="margin: 0;"> <span id="LC3670" class="line" lang="cpp"> <span class="n" style="color: #333;">branchCaches</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="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;">MemAllocate</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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">patternCount</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">stateSpaceDim</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cT</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">categoryCount</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="mi" style="color: #099;">64</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3728" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3726,7 +3728,7 @@ void _LikelihoodFunction::SetupLFCaches (void) {</td>
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<pre style="margin: 0;"> <span id="LC3728" class="line" lang="cpp"> <span class="p">}</span></span>
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3727
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3729
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<pre style="margin: 0;"> <span id="LC3729" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span> <span class="p">(</span><span class="n" style="color: #333;">columnBlock</span><span class="p">);</span> <span class="n" style="color: #333;">free</span> <span class="p">(</span><span class="n" style="color: #333;">translationCache</span><span class="p">);</span></span>
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3728
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3730
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<pre style="margin: 0;"> <span id="LC3730" class="line" lang="cpp"> <span class="n" style="color: #333;">conditionalTerminalNodeLikelihoodCaches</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ambigs</span><span class="p">;</span></span>
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3729
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<pre style="margin: 0;">-<span id="LC3729" class="line" lang="cpp"></span>
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3731
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<pre style="margin: 0;">+<span id="LC3731" class="line" lang="cpp"> <span class="n" style="color: #333;">errorTolerance</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAX</span> <span class="p">(</span><span class="mf" style="color: #099;">1.</span><span class="p">,</span><span class="n" style="color: #333;">round</span> <span class="p">(</span><span class="n" style="color: #333;">log</span> <span class="p">(</span><span class="mf" style="color: #099;">1.</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">maxFilterSize</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">log</span> <span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">)));</span></span>
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3730
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3732
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<pre style="margin: 0;"> <span id="LC3732" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef MDSOCL</span></span>
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3731
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<td class="diff-line-num new_line" data-linenumber="3733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3733
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<pre style="margin: 0;"> <span id="LC3733" class="line" lang="cpp"> <span class="n" style="color: #333;">OCLEval</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">patternCount</span><span class="p">,</span> <span class="n" style="color: #333;">theFilter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetDimension</span><span class="p">(),</span> <span class="n" style="color: #333;">conditionalInternalNodeLikelihoodCaches</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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3732
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3734
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<pre style="margin: 0;"> <span id="LC3734" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4110" style="width: 35px; color: rgba(0,0,0,0.3); 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="4112" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4110,8 +4112,12 @@ _Matrix* _LikelihoodFunction::Optimize (_AssociativeList const * options)</td>
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4110
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4112
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<pre style="margin: 0;"> <span id="LC4112" class="line" lang="cpp"> <span class="n" style="color: #333;">BenchmarkThreads</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="p">);</span></span>
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4111
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4113
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<pre style="margin: 0;"> <span id="LC4113" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __HYPHYMPI__</span></span>
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4112
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4114
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<pre style="margin: 0;"> <span id="LC4114" class="line" lang="cpp"> <span class="p">}</span></span>
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4115
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<pre style="margin: 0;">+<span id="LC4115" class="line" lang="cpp"> </span>
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4116
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<pre style="margin: 0;">+<span id="LC4116" class="line" lang="cpp"> </span>
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4113
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4117
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<pre style="margin: 0;"> <span id="LC4117" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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4114
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4118
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<pre style="margin: 0;"> <span id="LC4118" class="line" lang="cpp"></span>
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4119
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<pre style="margin: 0;">+<span id="LC4119" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//ObjectToConsole(variables_changed_during_last_compute);</span></span>
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4120
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<pre style="margin: 0;">+<span id="LC4120" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//NLToConsole();</span></span>
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4115
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4121
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<pre style="margin: 0;"> <span id="LC4121" class="line" lang="cpp"></span>
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4116
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4122
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<pre style="margin: 0;"> <span id="LC4122" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">skipCG</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">CheckEqual</span> <span class="p">(</span><span class="n" style="color: #333;">get_optimization_setting</span> <span class="p">(</span><span class="n" style="color: #333;">kSkipConjugateGradient</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">),</span> <span class="mf" style="color: #099;">0.0</span><span class="p">),</span></span>
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4117
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4123
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<pre style="margin: 0;"> <span id="LC4123" class="line" lang="cpp"> <span class="n" style="color: #333;">keepStartingPoint</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">CheckEqual</span> <span class="p">(</span><span class="n" style="color: #333;">get_optimization_setting</span> <span class="p">(</span><span class="n" style="color: #333;">kUseLastResults</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">),</span> <span class="mf" style="color: #099;">0.0</span><span class="p">),</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4128" style="width: 35px; color: rgba(0,0,0,0.3); 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="4134" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4128,14 +4134,23 @@ _Matrix* _LikelihoodFunction::Optimize (_AssociativeList const * options)</td>
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4128
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4134
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<pre style="margin: 0;"> <span id="LC4134" class="line" lang="cpp"> <span class="p">}</span></span>
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4129
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4135
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<pre style="margin: 0;"> <span id="LC4135" class="line" lang="cpp"> <span class="p">}</span></span>
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4130
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4136
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<pre style="margin: 0;"> <span id="LC4136" class="line" lang="cpp"> </span>
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4131
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<pre style="margin: 0;">-<span id="LC4131" class="line" lang="cpp"> </span>
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4137
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<pre style="margin: 0;">+<span id="LC4137" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0UL</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">indexInd</span><span class="p">.</span><span class="n" style="color: #333;">lLength</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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4138
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<pre style="margin: 0;">+<span id="LC4138" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">GetIthIndependentVar</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">varFlags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">HY_VARIABLE_CHANGED</span><span class="p">)</span> <span class="p">{</span></span>
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4139
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<pre style="margin: 0;">+<span id="LC4139" class="line" lang="cpp"> <span class="n" style="color: #333;">variables_changed_during_last_compute</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">InsertNumber</span> <span class="p">(</span><span class="n" style="color: #333;">GetIthIndependentVar</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_index</span><span class="p">());</span></span>
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4140
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<pre style="margin: 0;">+<span id="LC4140" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (variables_changed_during_last_compute->InsertNumber (GetIthIndependentVar(i)->get_index()) >= 0)</span></span>
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4141
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<pre style="margin: 0;">+<span id="LC4141" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// printf ("Insert [before] %s\n",GetIthIndependentName(i)->get_str());</span></span>
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4142
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<pre style="margin: 0;">+<span id="LC4142" class="line" lang="cpp"> <span class="p">}</span></span>
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4143
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<pre style="margin: 0;">+<span id="LC4143" class="line" lang="cpp"> <span class="p">}</span></span>
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4144
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<pre style="margin: 0;">+<span id="LC4144" class="line" lang="cpp"></span>
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4132
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4145
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<pre style="margin: 0;"> <span id="LC4145" class="line" lang="cpp"> <span class="n" style="color: #333;">_SimpleList</span> <span class="n" style="color: #333;">untag</span><span class="p">;</span></span>
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4133
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4146
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<pre style="margin: 0;"> <span id="LC4146" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">keepStartingPoint</span><span class="p">)</span> <span class="p">{</span></span>
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4134
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4147
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<pre style="margin: 0;"> <span id="LC4147" class="line" lang="cpp"> <span class="n" style="color: #333;">indexInd</span><span class="p">.</span><span class="n" style="color: #333;">Each</span> <span class="p">([</span><span class="k" style="font-weight: 600;">this</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">untag</span><span class="p">]</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">v</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="p">{</span></span>
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4135
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4148
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<pre style="margin: 0;"> <span id="LC4148" class="line" lang="cpp"> <span class="n" style="color: #333;">_Variable</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">iv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetIthIndependentVar</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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4149
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<pre style="margin: 0;">+<span id="LC4149" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf ("%s = %g, global %d, initialized %d, changed %d\n",GetIthIndependentName(i)->get_str(), GetIthIndependent(i), iv->IsGlobal(), iv->HasBeenInitialized(), iv->IsModified());</span></span>
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4136
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4150
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<pre style="margin: 0;"> <span id="LC4150" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">IsGlobal</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">HasBeenInitialized</span><span class="p">())</span> <span class="p">{</span></span>
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4137
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4151
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<pre style="margin: 0;"> <span id="LC4151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">IsModified</span><span class="p">())</span> <span class="p">{</span></span>
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4138
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4152
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<pre style="margin: 0;"> <span id="LC4152" class="line" lang="cpp"> <span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">MarkModified</span><span class="p">();</span></span>
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4153
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<pre style="margin: 0;">+<span id="LC4153" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf ("TAG [before] %s\n",GetIthIndependentName(i)->get_str());</span></span>
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4139
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4154
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<pre style="margin: 0;"> <span id="LC4154" class="line" lang="cpp"> <span class="n" style="color: #333;">untag</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC4155" class="line" lang="cpp"> <span class="p">}</span></span>
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4156
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<pre style="margin: 0;"> <span id="LC4156" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4148,12 +4163,11 @@ _Matrix* _LikelihoodFunction::Optimize (_AssociativeList const * options)</td>
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4148
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4163
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<pre style="margin: 0;"> <span id="LC4163" class="line" lang="cpp"></span>
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4149
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4164
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<pre style="margin: 0;"> <span id="LC4164" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">keepStartingPoint</span><span class="p">)</span> <span class="p">{</span></span>
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4150
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4165
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<pre style="margin: 0;"> <span id="LC4165" class="line" lang="cpp"> <span class="n" style="color: #333;">untag</span><span class="p">.</span><span class="n" style="color: #333;">Each</span> <span class="p">([</span><span class="k" style="font-weight: 600;">this</span><span class="p">]</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">v</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="p">{</span></span>
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4151
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<pre style="margin: 0;">-<span id="LC4151" class="line" lang="cpp"> <span class="n" style="color: #333;">_Variable</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">iv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetIthIndependentVar</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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4166
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<pre style="margin: 0;">+<span id="LC4166" class="line" lang="cpp"> <span class="n" style="color: #333;">_Variable</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">iv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetIthIndependentVar</span> <span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">);</span></span>
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4167
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<pre style="margin: 0;">+<span id="LC4167" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf ("UNTAG [before] %s\n",GetIthIndependentName(v)->get_str());</span></span>
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4152
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4168
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<pre style="margin: 0;"> <span id="LC4168" class="line" lang="cpp"> <span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ClearModified</span><span class="p">();</span></span>
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4153
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4169
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<pre style="margin: 0;"> <span id="LC4169" class="line" lang="cpp"> <span class="p">});</span></span>
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4154
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<pre style="margin: 0;">-<span id="LC4154" class="line" lang="cpp"> <span class="p">}</span></span>
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4155
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<pre style="margin: 0;">-<span id="LC4155" class="line" lang="cpp"></span>
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4156
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<pre style="margin: 0;">-<span id="LC4156" 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;">keepStartingPoint</span><span class="p">)</span> <span class="p">{</span></span>
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4170
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<pre style="margin: 0;">+<span id="LC4170" 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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4157
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4171
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<pre style="margin: 0;"> <span id="LC4171" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">global_starting_point</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_optimization_setting</span> <span class="p">(</span><span class="n" style="color: #333;">kGlobalStartingPoint</span><span class="p">,</span> <span class="mf" style="color: #099;">0.1</span><span class="p">);</span></span>
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4158
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4172
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<pre style="margin: 0;"> <span id="LC4172" class="line" lang="cpp"> </span>
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4159
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4173
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<pre style="margin: 0;"> <span id="LC4173" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">CheckEqual</span> <span class="p">(</span><span class="n" style="color: #333;">get_optimization_setting</span> <span class="p">(</span><span class="n" style="color: #333;">kRandomStartingPerturbations</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">),</span> <span class="mf" style="color: #099;">0.0</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4182" style="width: 35px; color: rgba(0,0,0,0.3); 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="4196" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4182,6 +4196,8 @@ _Matrix* _LikelihoodFunction::Optimize (_AssociativeList const * options)</td>
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4182
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4196
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<pre style="margin: 0;"> <span id="LC4196" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0UL</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">indexInd</span><span class="p">.</span><span class="n" style="color: #333;">lLength</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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4183
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4197
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<pre style="margin: 0;"> <span id="LC4197" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">GetIthIndependentVar</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">varFlags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">HY_VARIABLE_CHANGED</span><span class="p">)</span> <span class="p">{</span></span>
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4184
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4198
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<pre style="margin: 0;"> <span id="LC4198" class="line" lang="cpp"> <span class="n" style="color: #333;">variables_changed_during_last_compute</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">InsertNumber</span> <span class="p">(</span><span class="n" style="color: #333;">GetIthIndependentVar</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_index</span><span class="p">());</span></span>
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4199
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<pre style="margin: 0;">+<span id="LC4199" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (variables_changed_during_last_compute->InsertNumber (GetIthIndependentVar(i)->get_index()) >= 0)</span></span>
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4200
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<pre style="margin: 0;">+<span id="LC4200" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// printf ("Insert [after] %s\n",GetIthIndependentName(i)->get_str());</span></span>
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4185
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4201
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<pre style="margin: 0;"> <span id="LC4201" class="line" lang="cpp"> <span class="p">}</span></span>
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4186
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4202
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<pre style="margin: 0;"> <span id="LC4202" class="line" lang="cpp"> <span class="p">}</span></span>
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4187
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4203
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<pre style="margin: 0;"> <span id="LC4203" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5645" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -5629,7 +5645,7 @@ long _LikelihoodFunction::Bracket (long index, hyFloat& left, hyFloat& middle</td>
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5629
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5645
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<pre style="margin: 0;"> <span id="LC5645" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> (or involves a paremeter that has very little effect on the LF), recomputation could be within numerical error</span></span>
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5630
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5646
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<pre style="margin: 0;"> <span id="LC5646" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> </span></span>
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5631
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5647
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<pre style="margin: 0;"> <span id="LC5647" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> **/</span></span>
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5632
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<pre style="margin: 0;">-<span id="LC5632" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rightValue</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">middleValue</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">1e-<span class="idiff left">9</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">leftValue</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">middleValue</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff right">1e-9</span></span><span class="p">)</span> <span class="p">{</span></span>
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5648
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<pre style="margin: 0;">+<span id="LC5648" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rightValue</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">middleValue</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">1e-<span class="idiff left">12</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">errorTolerance</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">leftValue</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">middleValue</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">1e-12</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">errorTolerance</span></span><span class="p">)</span> <span class="p">{</span></span>
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5649
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<pre style="margin: 0;"> <span id="LC5649" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">buf</span><span class="p">[</span><span class="mi" style="color: #099;">256</span><span class="p">],</span> <span class="n" style="color: #333;">buf2</span><span class="p">[</span><span class="mi" style="color: #099;">512</span><span class="p">];</span></span>
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5634
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5650
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<pre style="margin: 0;"> <span id="LC5650" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span> <span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">,</span> <span class="mi" style="color: #099;">256</span><span class="p">,</span> <span class="s" style="color: #d14;">" </span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">ERROR: [_LikelihoodFunction::Bracket (index %ld) recomputed the value to midpoint: L(%g) = %g [@%g -> %g:@%g -> %g]]"</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">middle</span><span class="p">,</span> <span class="n" style="color: #333;">middleValue</span><span class="p">,</span> <span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="n" style="color: #333;">leftValue</span><span class="p">,</span><span class="n" style="color: #333;">right</span><span class="p">,</span> <span class="n" style="color: #333;">rightValue</span><span class="p">);</span></span>
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5635
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5651
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<pre style="margin: 0;"> <span id="LC5651" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span> <span class="p">(</span><span class="n" style="color: #333;">buf2</span><span class="p">,</span> <span class="mi" style="color: #099;">512</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">[_LikelihoodFunction::Bracket (index %ld) BRACKET %s: %20.16g <= %20.16g >= %20.16g. steps, L=%g, R=%g, values %15.12g : %15.12g - %15.12g]"</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">successful</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"SUCCESSFUL"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"FAILED"</span><span class="p">,</span> <span class="n" style="color: #333;">left</span><span class="p">,</span><span class="n" style="color: #333;">middle</span><span class="p">,</span><span class="n" style="color: #333;">right</span><span class="p">,</span> <span class="n" style="color: #333;">leftStep</span><span class="p">,</span> <span class="n" style="color: #333;">rightStep</span><span class="p">,</span> <span class="n" style="color: #333;">leftValue</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">middleValue</span><span class="p">,</span> <span class="n" style="color: #333;">middleValue</span><span class="p">,</span> <span class="n" style="color: #333;">rightValue</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">middleValue</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6500,7 +6516,7 @@ hyFloat _LikelihoodFunction::ConjugateGradientDescent (hyFloat step_precision</td>
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6516
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<pre style="margin: 0;"> <span id="LC6516" class="line" lang="cpp"> <span class="p">}</span></span>
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6501
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6517
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<pre style="margin: 0;"> <span id="LC6517" class="line" lang="cpp"></span>
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6518
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<pre style="margin: 0;"> <span id="LC6518" class="line" lang="cpp"> <span class="n" style="color: #333;">SetAllIndependent</span> <span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bestVal</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC6503" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maxSoFar</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">initial_value</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">CheckEqual</span><span class="p">(</span><span class="n" style="color: #333;">maxSoFar</span><span class="p">,</span> <span class="n" style="color: #333;">initial_value</span><span class="p">,</span> <span class="n" style="color: #333;">kMachineEpsilon</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;"><span class="idiff left right">100.</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6519
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<pre style="margin: 0;">+<span id="LC6519" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maxSoFar</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">initial_value</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">CheckEqual</span><span class="p">(</span><span class="n" style="color: #333;">maxSoFar</span><span class="p">,</span> <span class="n" style="color: #333;">initial_value</span><span class="p">,</span> <span class="n" style="color: #333;">kMachineEpsilon</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;"><span class="idiff left right">errorTolerance</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="p">{</span></span>
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6504
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6520
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<pre style="margin: 0;"> <span id="LC6520" class="line" lang="cpp"> <span class="n" style="color: #333;">HandleApplicationError</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span><span class="p">(</span><span class="s" style="color: #d14;">"Internal optimization error in _LikelihoodFunction::ConjugateGradientDescent. Worsened likelihood score from "</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">initial_value</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">" to "</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">maxSoFar</span><span class="p">);</span></span>
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6505
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6521
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<pre style="margin: 0;"> <span id="LC6521" class="line" lang="cpp"> <span class="p">}</span></span>
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6506
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6522
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<pre style="margin: 0;"> <span id="LC6522" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6874" style="width: 35px; color: rgba(0,0,0,0.3); 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="6890" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6874,7 +6890,7 @@ void _LikelihoodFunction::GradientDescent (hyFloat& gPrecision, _Matrix& best</td>
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6874
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6890
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<pre style="margin: 0;"> <span id="LC6890" class="line" lang="cpp"> <span class="n" style="color: #333;">bestVal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_best_vector</span><span class="p">;</span></span>
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6875
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6891
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<pre style="margin: 0;"> <span id="LC6891" class="line" lang="cpp"> <span class="p">}</span></span>
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6876
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6892
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<pre style="margin: 0;"> <span id="LC6892" class="line" lang="cpp"></span>
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6877
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<pre style="margin: 0;">-<span id="LC6877" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maxSoFar</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">initialValue</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">CheckEqual</span> <span class="p">(</span><span class="n" style="color: #333;">maxSoFar</span><span class="p">,</span> <span class="n" style="color: #333;">initialValue</span><span class="p">,</span> <span class="mf" style="color: #099;"><span class="idiff left">100.</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">kMachineEpsilon</span></span><span class="p">))</span> <span class="p">{</span></span>
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6893
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<pre style="margin: 0;">+<span id="LC6893" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maxSoFar</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">initialValue</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">CheckEqual</span> <span class="p">(</span><span class="n" style="color: #333;">maxSoFar</span><span class="p">,</span> <span class="n" style="color: #333;">initialValue</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">kMachineEpsilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">errorTolerance</span></span><span class="p">))</span> <span class="p">{</span></span>
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6878
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6894
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<pre style="margin: 0;"> <span id="LC6894" class="line" lang="cpp"> <span class="n" style="color: #333;">_TerminateAndDump</span><span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">" _LikelihoodFunction::GradientLocateTheBump: in the Brent loop iteration "</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">(</span><span class="n" style="color: #333;">outcome</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">". "</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="n" style="color: #333;">maxSoFar</span><span class="p">,</span> <span class="s" style="color: #d14;">"%18.16g"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">" / "</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="n" style="color: #333;">initialValue</span><span class="p">,</span><span class="s" style="color: #d14;">"%18.16g"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">".</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> Optimization direction: </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">_String</span> <span class="p">((</span><span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">gradient</span><span class="p">.</span><span class="n" style="color: #333;">toStr</span><span class="p">())</span> <span class="p">);</span></span>
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6879
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6895
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<pre style="margin: 0;"> <span id="LC6895" class="line" lang="cpp"></span>
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6880
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6896
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<pre style="margin: 0;"> <span id="LC6896" 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="diff-line-num unfold js-unfold old_line" data-linenumber="7081" style="width: 35px; color: rgba(0,0,0,0.3); 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="7097" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -7081,7 +7097,7 @@ void _LikelihoodFunction::LocateTheBump (long index,hyFloat gPrecision, hyFlo</td>
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7081
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7097
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<pre style="margin: 0;"> <span id="LC7097" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span> <span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">,</span> <span class="mi" style="color: #099;">256</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">[_LikelihoodFunction::LocateTheBump (index %ld) RESETTING THE VALUE (worse log likelihood obtained; current value %20.16g, best value %20.16g) ]</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">GetIthIndependent</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">),</span> <span class="n" style="color: #333;">bestVal</span><span class="p">);</span></span>
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7082
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7098
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<pre style="margin: 0;"> <span id="LC7098" class="line" lang="cpp"> <span class="n" style="color: #333;">BufferToConsole</span> <span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">);</span></span>
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7083
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7099
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<pre style="margin: 0;"> <span id="LC7099" class="line" lang="cpp"> <span class="p">}</span></span>
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7084
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<pre style="margin: 0;">-<span id="LC7084" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">CheckEqual</span><span class="p">(</span><span class="n" style="color: #333;">GetIthIndependent</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">),</span> <span class="n" style="color: #333;">bestVal</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">fabs</span> <span class="p">(</span><span class="n" style="color: #333;">middleValue</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">maxSoFar</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">1e-<span class="idiff left right">9</span></span><span class="p">)</span> <span class="p">{</span></span>
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7100
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<pre style="margin: 0;">+<span id="LC7100" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">CheckEqual</span><span class="p">(</span><span class="n" style="color: #333;">GetIthIndependent</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">),</span> <span class="n" style="color: #333;">bestVal</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">fabs</span> <span class="p">(</span><span class="n" style="color: #333;">middleValue</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">maxSoFar</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">1e-<span class="idiff left">12</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">errorTolerance</span></span><span class="p">)</span> <span class="p">{</span></span>
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7085
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7101
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<pre style="margin: 0;"> <span id="LC7101" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">buf</span><span class="p">[</span><span class="mi" style="color: #099;">256</span><span class="p">];</span></span>
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7086
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7102
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<pre style="margin: 0;"> <span id="LC7102" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span> <span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">,</span> <span class="mi" style="color: #099;">256</span><span class="p">,</span> <span class="s" style="color: #d14;">" </span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">ERROR: [_LikelihoodFunction::LocateTheBump (index %ld) current value %20.16g (parameter = %20.16g), best value %20.16g (parameter = %20.16g)); delta = %20.16g ]</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">middleValue</span><span class="p">,</span> <span class="n" style="color: #333;">GetIthIndependent</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">),</span> <span class="n" style="color: #333;">maxSoFar</span><span class="p">,</span> <span class="n" style="color: #333;">bestVal</span><span class="p">,</span> <span class="n" style="color: #333;">maxSoFar</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">middleValue</span><span class="p">);</span></span>
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7087
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7103
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<pre style="margin: 0;"> <span id="LC7103" class="line" lang="cpp"> <span class="n" style="color: #333;">_TerminateAndDump</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Parameter name "</span> <span class="o" style="font-weight: 600;">&</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">GetIthIndependentName</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">));</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/e5c8fd32984d059ec09233aa8f7e5cdb888c538c#81843dd3cf849d08e0f197d837dd373534c7c756"><strong>src/core/matrix.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1895,7 +1895,7 @@ bool _Matrix::AmISparseFast (_Matrix& whereTo) {</td>
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1895
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1895
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<pre style="margin: 0;"> <span id="LC1895" class="line" lang="cpp"> </span>
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1896
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1896
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<pre style="margin: 0;"> <span id="LC1896" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">non_zero_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">alloca</span> <span class="p">(</span><span class="n" style="color: #333;">threshold</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">));</span></span>
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1897
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<pre style="margin: 0;"> <span id="LC1897" class="line" lang="cpp"> </span>
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1898
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<pre style="margin: 0;">-<span id="LC1898" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if<span class="idiff left right">def</span> _SLKP_USE_AVX_INTRINSICS</span></span>
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1898
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<pre style="margin: 0;">+<span id="LC1898" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if<span class="idiff left right"> defined</span> _SLKP_USE_AVX_INTRINSICS</span></span>
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1899
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1899
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<pre style="margin: 0;"> <span id="LC1899" class="line" lang="cpp"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">zeros</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_setzero_pd</span><span class="p">();</span></span>
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1900
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1900
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<pre style="margin: 0;"> <span id="LC1900" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">lDimMOD4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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1901
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1901
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<pre style="margin: 0;"> <span id="LC1901" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">lDimMOD4</span><span class="p">;</span> <span class="n" style="color: #333;">i</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>
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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">@@ -1917,6 +1917,27 @@ bool _Matrix::AmISparseFast (_Matrix& whereTo) {</td>
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1917
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1917
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<pre style="margin: 0;"> <span id="LC1917" class="line" lang="cpp"> <span class="p">}</span></span>
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1918
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1918
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<pre style="margin: 0;"> <span id="LC1918" class="line" lang="cpp"> <span class="p">}</span></span>
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1919
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1919
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<pre style="margin: 0;"> <span id="LC1919" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1920" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#elif _SLKP_USE_ARM_NEON</span></span>
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1921
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<pre style="margin: 0;">+<span id="LC1921" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">zeros</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdupq_n_f64</span> <span class="p">(</span><span class="mf" style="color: #099;">0.</span><span class="p">);</span></span>
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1922
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<pre style="margin: 0;">+<span id="LC1922" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">lDimMOD2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1923
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<pre style="margin: 0;">+<span id="LC1923" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">lDimMOD2</span><span class="p">;</span> <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 class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1924
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<pre style="margin: 0;">+<span id="LC1924" class="line" lang="cpp"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1925
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<pre style="margin: 0;">+<span id="LC1925" class="line" lang="cpp"> <span class="n" style="color: #333;">uint64x2_t</span> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vceqq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">vld1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">),</span> <span class="n" style="color: #333;">zeros</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1926
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<pre style="margin: 0;">+<span id="LC1926" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vaddvq_u64</span> <span class="p">(</span><span class="n" style="color: #333;">res</span><span class="p">))</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// something is different</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1927
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<pre style="margin: 0;">+<span id="LC1927" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vgetq_lane_u64</span> <span class="p">(</span><span class="n" style="color: #333;">res</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="p">{</span> <span class="n" style="color: #333;">non_zero_index</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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span> <span class="k" style="font-weight: 600;">if</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;">threshold</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="p">};</span></span>
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1928
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<pre style="margin: 0;">+<span id="LC1928" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vgetq_lane_u64</span> <span class="p">(</span><span class="n" style="color: #333;">res</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="p">{</span> <span class="n" style="color: #333;">non_zero_index</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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="k" style="font-weight: 600;">if</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;">threshold</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="p">};</span></span>
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1929
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<pre style="margin: 0;">+<span id="LC1929" class="line" lang="cpp"> <span class="p">}</span></span>
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1930
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<pre style="margin: 0;">+<span id="LC1930" class="line" lang="cpp"> <span class="p">}</span></span>
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1931
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<pre style="margin: 0;">+<span id="LC1931" class="line" lang="cpp"> </span>
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1932
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<pre style="margin: 0;">+<span id="LC1932" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">threshold</span><span class="p">)</span></span>
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1933
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<pre style="margin: 0;">+<span id="LC1933" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lDimMOD2</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;">lDim</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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1934
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<pre style="margin: 0;">+<span id="LC1934" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">theData</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="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="p">{</span></span>
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1935
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<pre style="margin: 0;">+<span id="LC1935" class="line" lang="cpp"> <span class="n" style="color: #333;">non_zero_index</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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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1936
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<pre style="margin: 0;">+<span id="LC1936" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">threshold</span><span class="p">)</span> <span class="p">{</span></span>
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1937
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<pre style="margin: 0;">+<span id="LC1937" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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1938
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<pre style="margin: 0;">+<span id="LC1938" class="line" lang="cpp"> <span class="p">}</span></span>
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1939
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<pre style="margin: 0;">+<span id="LC1939" class="line" lang="cpp"> <span class="p">}</span></span>
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1940
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<pre style="margin: 0;">+<span id="LC1940" class="line" lang="cpp"> <span class="p">}</span></span>
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1920
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1941
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<pre style="margin: 0;"> <span id="LC1941" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1921
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1942
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<pre style="margin: 0;"> <span id="LC1942" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">lDim</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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1922
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1943
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<pre style="margin: 0;"> <span id="LC1943" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">theData</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="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3357" style="width: 35px; color: rgba(0,0,0,0.3); 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="3378" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3357,8 +3378,8 @@ void _Matrix::AddMatrix (_Matrix& storage, _Matrix& secondArg, bool subtract</td>
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3357
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3378
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<pre style="margin: 0;"> <span id="LC3378" class="line" lang="cpp"> </span>
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3358
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3379
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<pre style="margin: 0;"> <span id="LC3379" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">subtract</span><span class="p">)</span> <span class="p">{</span></span>
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3359
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3380
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<pre style="margin: 0;"> <span id="LC3380" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_AVX_INTRINSICS</span></span>
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3360
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<td class="diff-line-num new_line old" data-linenumber="3381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3360" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="cp" style="color: #999; font-weight: 600;">#define CELL_OP1(x,y) __m256d y = _mm256_sub_pd (_mm256_loadu_pd (stData+x), _mm256_loadu_pd (argData+x))</span></span>
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3361
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<td class="diff-line-num new_line old" data-linenumber="3381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3361" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define CELL_OP2(x,y) _mm256_storeu_pd (stData+x,y)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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3381
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<pre style="margin: 0;">+<span id="LC3381" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define CELL_OP1(x,y) __m256d y = _mm256_sub_pd (_mm256_loadu_pd (stData+x), _mm256_loadu_pd (argData+x))</span></span>
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3382
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<pre style="margin: 0;">+<span id="LC3382" class="line" lang="cpp"><span class="idiff left right"> </span><span class="cp" style="color: #999; font-weight: 600;">#define CELL_OP2(x,y) _mm256_storeu_pd (stData+x,y)</span></span>
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3362
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3383
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<pre style="margin: 0;"> <span id="LC3383" class="line" lang="cpp"> </span>
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3363
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3384
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<pre style="margin: 0;"> <span id="LC3384" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>
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3364
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3385
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<pre style="margin: 0;"> <span id="LC3385" 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="diff-line-num unfold js-unfold old_line" data-linenumber="3376" style="width: 35px; color: rgba(0,0,0,0.3); 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="3397" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3376,6 +3397,26 @@ void _Matrix::AddMatrix (_Matrix& storage, _Matrix& secondArg, bool subtract</td>
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3376
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3397
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<pre style="margin: 0;"> <span id="LC3397" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP2</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="n" style="color: #333;">r3</span><span class="p">);</span></span>
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3377
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3398
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<pre style="margin: 0;"> <span id="LC3398" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP2</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;">12</span><span class="p">,</span><span class="n" style="color: #333;">r4</span><span class="p">);</span></span>
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3378
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3399
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<pre style="margin: 0;"> <span id="LC3399" class="line" lang="cpp"> <span class="p">}</span></span>
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3400
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<pre style="margin: 0;">+<span id="LC3400" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#elif defined _SLKP_USE_ARM_NEON</span></span>
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3401
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<pre style="margin: 0;">+<span id="LC3401" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define CELL_OP1(x,y) float64x2_t y = vsubq_f64 (vld1q_f64 (stData+x), vld1q_f64 (argData+x))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3402
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<pre style="margin: 0;">+<span id="LC3402" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define CELL_OP2(x,y) vst1q_f64 (stData+x,y)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3403
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<pre style="margin: 0;">+<span id="LC3403" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>
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3404
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<pre style="margin: 0;">+<span id="LC3404" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop vectorize(enable)</span></span>
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3405
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<pre style="margin: 0;">+<span id="LC3405" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop interleave(enable)</span></span>
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3406
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<pre style="margin: 0;">+<span id="LC3406" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop unroll(enable)</span></span>
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3407
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<pre style="margin: 0;">+<span id="LC3407" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC ivdep</span></span>
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3408
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<pre style="margin: 0;">+<span id="LC3408" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma ivdep</span></span>
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3409
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<pre style="margin: 0;">+<span id="LC3409" 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>
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3410
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<pre style="margin: 0;">+<span id="LC3410" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">,</span><span class="n" style="color: #333;">r1</span><span class="p">);</span></span>
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3411
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<pre style="margin: 0;">+<span id="LC3411" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP1</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;">2</span><span class="p">,</span><span class="n" style="color: #333;">r2</span><span class="p">);</span></span>
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3412
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<pre style="margin: 0;">+<span id="LC3412" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP1</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;">4</span><span class="p">,</span><span class="n" style="color: #333;">r3</span><span class="p">);</span></span>
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3413
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<pre style="margin: 0;">+<span id="LC3413" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP1</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;">6</span><span class="p">,</span><span class="n" style="color: #333;">r4</span><span class="p">);</span></span>
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3414
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<pre style="margin: 0;">+<span id="LC3414" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">,</span><span class="n" style="color: #333;">r1</span><span class="p">);</span></span>
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3415
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<pre style="margin: 0;">+<span id="LC3415" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP2</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;">2</span><span class="p">,</span><span class="n" style="color: #333;">r2</span><span class="p">);</span></span>
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3416
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<pre style="margin: 0;">+<span id="LC3416" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP2</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;">4</span><span class="p">,</span><span class="n" style="color: #333;">r3</span><span class="p">);</span></span>
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3417
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<pre style="margin: 0;">+<span id="LC3417" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP2</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;">6</span><span class="p">,</span><span class="n" style="color: #333;">r4</span><span class="p">);</span></span>
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3418
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<pre style="margin: 0;">+<span id="LC3418" class="line" lang="cpp"> <span class="p">}</span></span>
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3419
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<pre style="margin: 0;">+<span id="LC3419" class="line" lang="cpp"> </span>
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3379
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3420
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<pre style="margin: 0;"> <span id="LC3420" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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3380
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3421
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<pre style="margin: 0;"> <span id="LC3421" 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;">4</span><span class="p">)</span> <span class="p">{</span></span>
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3381
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3422
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<pre style="margin: 0;"> <span id="LC3422" class="line" lang="cpp"> <span class="n" style="color: #333;">stData</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">]</span><span class="o" style="font-weight: 600;">-=</span><span class="n" style="color: #333;">argData</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3400" style="width: 35px; color: rgba(0,0,0,0.3); 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="3441" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3400,7 +3441,27 @@ void _Matrix::AddMatrix (_Matrix& storage, _Matrix& secondArg, bool subtract</td>
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3400
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3441
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<pre style="margin: 0;"> <span id="LC3441" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</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;">12</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC3442" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC3443" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC3403" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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3444
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<pre style="margin: 0;">+<span id="LC3444" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#elif defined _SLKP_USE_ARM_NEON</span></span>
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<pre style="margin: 0;">+<span id="LC3445" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define CELL_OP1(x,y) float64x2_t y = vaddq_f64 (vld1q_f64 (stData+x), vld1q_f64 (argData+x))</span></span>
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3446
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<pre style="margin: 0;">+<span id="LC3446" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define CELL_OP2(x,y) vst1q_f64 (stData+x,y)</span></span>
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<pre style="margin: 0;">+<span id="LC3447" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>
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3448
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<pre style="margin: 0;">+<span id="LC3448" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop vectorize(enable)</span></span>
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3449
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<pre style="margin: 0;">+<span id="LC3449" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop interleave(enable)</span></span>
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<pre style="margin: 0;">+<span id="LC3450" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop unroll(enable)</span></span>
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3451
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<pre style="margin: 0;">+<span id="LC3451" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC ivdep</span></span>
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3452
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<pre style="margin: 0;">+<span id="LC3452" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma ivdep</span></span>
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3453
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<pre style="margin: 0;">+<span id="LC3453" 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>
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3454
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<pre style="margin: 0;">+<span id="LC3454" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">,</span><span class="n" style="color: #333;">r1</span><span class="p">);</span></span>
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3455
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<pre style="margin: 0;">+<span id="LC3455" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP1</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;">2</span><span class="p">,</span><span class="n" style="color: #333;">r2</span><span class="p">);</span></span>
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3456
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<pre style="margin: 0;">+<span id="LC3456" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP1</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;">4</span><span class="p">,</span><span class="n" style="color: #333;">r3</span><span class="p">);</span></span>
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3457
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<pre style="margin: 0;">+<span id="LC3457" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP1</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;">6</span><span class="p">,</span><span class="n" style="color: #333;">r4</span><span class="p">);</span></span>
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3458
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<pre style="margin: 0;">+<span id="LC3458" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">,</span><span class="n" style="color: #333;">r1</span><span class="p">);</span></span>
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3459
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<pre style="margin: 0;">+<span id="LC3459" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP2</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;">2</span><span class="p">,</span><span class="n" style="color: #333;">r2</span><span class="p">);</span></span>
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3460
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<pre style="margin: 0;">+<span id="LC3460" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP2</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;">4</span><span class="p">,</span><span class="n" style="color: #333;">r3</span><span class="p">);</span></span>
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3461
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<pre style="margin: 0;">+<span id="LC3461" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP2</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;">6</span><span class="p">,</span><span class="n" style="color: #333;">r4</span><span class="p">);</span></span>
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3462
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<pre style="margin: 0;">+<span id="LC3462" class="line" lang="cpp"> <span class="p">}</span></span>
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3463
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<pre style="margin: 0;">+<span id="LC3463" class="line" lang="cpp"> </span>
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3464
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<pre style="margin: 0;">+<span id="LC3464" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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3404
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3465
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<pre style="margin: 0;"> <span id="LC3465" 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;">4</span><span class="p">)</span> <span class="p">{</span></span>
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3405
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3466
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<pre style="margin: 0;"> <span id="LC3466" class="line" lang="cpp"> <span class="n" style="color: #333;">stData</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">]</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">argData</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">];</span></span>
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3406
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3467
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<pre style="margin: 0;"> <span id="LC3467" class="line" lang="cpp"> <span class="n" style="color: #333;">stData</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;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">argData</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;">1</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">@@ -3630,6 +3691,21 @@ void _Matrix::Multiply (_Matrix& storage, hyFloat c)</td>
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3630
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3691
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<pre style="margin: 0;"> <span id="LC3691" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</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;">lDim</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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3631
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3692
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<pre style="margin: 0;"> <span id="LC3692" class="line" lang="cpp"> <span class="n" style="color: #333;">destination</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;">source</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;">c</span><span class="p">;</span></span>
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3632
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3693
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<pre style="margin: 0;"> <span id="LC3693" class="line" lang="cpp"> <span class="p">}</span></span>
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3694
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<pre style="margin: 0;">+<span id="LC3694" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#elif defined _SLKP_USE_ARM_NEON</span></span>
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3695
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<pre style="margin: 0;">+<span id="LC3695" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define CELL_OP(k) vst1q_f64 (destination + k, vmulq_f64(value_op, vld1q_f64 (source+k)))</span></span>
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3696
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<pre style="margin: 0;">+<span id="LC3696" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">lDimM8</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span></span>
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3697
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<pre style="margin: 0;">+<span id="LC3697" class="line" lang="cpp"> <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>
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3698
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<pre style="margin: 0;">+<span id="LC3698" class="line" lang="cpp"> </span>
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3699
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<pre style="margin: 0;">+<span id="LC3699" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">value_op</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdupq_n_f64</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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3700
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<pre style="margin: 0;">+<span id="LC3700" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</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;">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;">lDimM8</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;">8</span><span class="p">)</span> <span class="p">{</span></span>
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3701
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<pre style="margin: 0;">+<span id="LC3701" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span> <span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">);</span></span>
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3702
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<pre style="margin: 0;">+<span id="LC3702" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</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>
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3703
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<pre style="margin: 0;">+<span id="LC3703" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</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>
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3704
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<pre style="margin: 0;">+<span id="LC3704" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</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;">6</span><span class="p">);</span></span>
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3705
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<pre style="margin: 0;">+<span id="LC3705" class="line" lang="cpp"> <span class="p">}</span></span>
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3706
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<pre style="margin: 0;">+<span id="LC3706" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</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;">lDim</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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3707
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<pre style="margin: 0;">+<span id="LC3707" class="line" lang="cpp"> <span class="n" style="color: #333;">destination</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;">source</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;">c</span><span class="p">;</span></span>
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3708
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<pre style="margin: 0;">+<span id="LC3708" class="line" lang="cpp"> <span class="p">}</span></span>
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3633
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3709
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<pre style="margin: 0;"> <span id="LC3709" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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3634
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3710
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<pre style="margin: 0;"> <span id="LC3710" 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;">lDim</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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3635
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3711
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<pre style="margin: 0;"> <span id="LC3711" class="line" lang="cpp"> <span class="n" style="color: #333;">destination</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;">source</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;">c</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3730" style="width: 35px; color: rgba(0,0,0,0.3); 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="3806" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3730,11 +3806,14 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix const& secondArg) const</td>
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3730
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3806
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<pre style="margin: 0;"> <span id="LC3806" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#elif _SLKP_USE_SSE_INTRINSICS</span></span>
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3731
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3807
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<pre style="margin: 0;"> <span id="LC3807" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define DO_GROUP_OP1(X,Y,k) X = _mm_loadu_pd(dest + row_offset + k); Y = _mm_loadu_pd(secondArg.theData + col_offset + k); X = _mm_add_pd (X, _mm_mul_pd(A4, Y));</span></span>
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3732
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3808
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<pre style="margin: 0;"> <span id="LC3808" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define DO_GROUP_OP2(X,k) _mm_storeu_pd (dest + row_offset + k,X);</span></span>
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3809
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<pre style="margin: 0;">+<span id="LC3809" class="line" lang="cpp"> </span>
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3810
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<pre style="margin: 0;">+<span id="LC3810" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#elif _SLKP_USE_ARM_NEON</span></span>
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3811
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<pre style="margin: 0;">+<span id="LC3811" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define DO_GROUP_OP1(X,Y,k) X = vld1q_f64 (dest + row_offset + k); Y = vld1q_f64 (secondArg.theData + col_offset + k); X = vfmaq_f64 (X, A4, Y);</span></span>
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3812
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<pre style="margin: 0;">+<span id="LC3812" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define DO_GROUP_OP2(X,k) vst1q_f64 (dest + row_offset + k,X);</span></span>
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3733
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3813
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<pre style="margin: 0;"> <span id="LC3813" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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3734
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3814
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<pre style="margin: 0;"> <span id="LC3814" class="line" lang="cpp"></span>
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3735
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3815
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<pre style="margin: 0;"> <span id="LC3815" class="line" lang="cpp"> </span>
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3736
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3816
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<pre style="margin: 0;"> <span id="LC3816" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef _SLKP_SSE_VECTORIZATION_</span></span>
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3737
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<pre style="margin: 0;">-<span id="LC3737" class="line" lang="cpp"> </span>
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3738
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3817
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<pre style="margin: 0;"> <span id="LC3817" class="line" lang="cpp"> </span>
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3739
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3818
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<pre style="margin: 0;"> <span id="LC3818" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dimm4</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>
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3740
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<td class="diff-line-num new_line" data-linenumber="3819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3819
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<pre style="margin: 0;"> <span id="LC3819" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3818" style="width: 35px; color: rgba(0,0,0,0.3); 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="3897" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3818,7 +3897,7 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix const& secondArg) const</td>
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3818
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3897
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<pre style="margin: 0;"> <span id="LC3897" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="3819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3819
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<td class="diff-line-num new_line" data-linenumber="3898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3898
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<pre style="margin: 0;"> <span id="LC3898" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="3820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3820
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<td class="diff-line-num new_line" data-linenumber="3899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3899
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<pre style="margin: 0;"> <span id="LC3899" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#elif _SLKP_USE_SSE_INTRINSICS</span></span>
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3821
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<td class="diff-line-num new_line old" data-linenumber="3900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3821" class="line" lang="cpp"> <span class="n" style="color: #333;">memset</span> <span class="p">(</span><span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">*</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>
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<td class="diff-line-num new old_line" data-linenumber="3822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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3900
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<pre style="margin: 0;">+<span id="LC3900" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">memset</span> <span class="p">(</span><span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">*</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>
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<td class="diff-line-num old_line" data-linenumber="3822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3822
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<td class="diff-line-num new_line" data-linenumber="3901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3901
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<pre style="margin: 0;"> <span id="LC3901" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">ti</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="3823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3823
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<td class="diff-line-num new_line" data-linenumber="3902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3902
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<pre style="margin: 0;"> <span id="LC3902" class="line" lang="cpp"> <span class="n" style="color: #333;">row_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="3824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3824
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<td class="diff-line-num new_line" data-linenumber="3903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3903
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<pre style="margin: 0;"> <span id="LC3903" class="line" lang="cpp"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3869" style="width: 35px; color: rgba(0,0,0,0.3); 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="3948" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3869,6 +3948,58 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix const& secondArg) const</td>
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3869
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3948
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<pre style="margin: 0;"> <span id="LC3948" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="3870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3870
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<td class="diff-line-num new_line" data-linenumber="3949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3949
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<pre style="margin: 0;"> <span id="LC3949" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="3871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3871
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<td class="diff-line-num new_line" data-linenumber="3950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3950
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<pre style="margin: 0;"> <span id="LC3950" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3951
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<pre style="margin: 0;">+<span id="LC3951" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#elif _SLKP_USE_ARM_NEON</span></span>
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3952
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<pre style="margin: 0;">+<span id="LC3952" class="line" lang="cpp"> <span class="n" style="color: #333;">memset</span> <span class="p">(</span><span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">*</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>
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3953
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<pre style="margin: 0;">+<span id="LC3953" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">ti</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">,</span></span>
</pre>
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3954
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<pre style="margin: 0;">+<span id="LC3954" class="line" lang="cpp"> <span class="n" style="color: #333;">row_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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3955
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<pre style="margin: 0;">+<span id="LC3955" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="3956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3956
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<pre style="margin: 0;">+<span id="LC3956" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vDim</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">20UL</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3957
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<pre style="margin: 0;">+<span id="LC3957" 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;">0</span><span class="p">;</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">20</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="n" style="color: #333;">row_offset</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">20</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3958
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<pre style="margin: 0;">+<span id="LC3958" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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3959
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<pre style="margin: 0;">+<span id="LC3959" 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="mi" style="color: #099;">20L</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;">ti</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">20L</span><span class="p">)</span> <span class="p">{</span></span>
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3960
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<pre style="margin: 0;">+<span id="LC3960" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">A4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdupq_n_f64</span><span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]);</span></span>
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3961
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<pre style="margin: 0;">+<span id="LC3961" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//for (long k = 0; k < 20L; k+=4) {</span></span>
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3962
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<pre style="margin: 0;">+<span id="LC3962" 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 class="n" style="color: #333;">D4_1</span><span class="p">,</span> <span class="n" style="color: #333;">B4_1</span><span class="p">,</span> <span class="n" style="color: #333;">D4_2</span><span class="p">,</span> <span class="n" style="color: #333;">B4_2</span><span class="p">,</span> <span class="n" style="color: #333;">D4_3</span><span class="p">,</span> <span class="n" style="color: #333;">B4_3</span><span class="p">,</span> <span class="n" style="color: #333;">D4_4</span><span class="p">,</span> <span class="n" style="color: #333;">B4_4</span><span class="p">;</span></span>
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3963
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<pre style="margin: 0;">+<span id="LC3963" 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="mi" style="color: #099;">0</span><span class="p">);</span></span>
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3964
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<pre style="margin: 0;">+<span id="LC3964" 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_1</span><span class="p">,</span> <span class="n" style="color: #333;">B4_1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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3965
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<pre style="margin: 0;">+<span id="LC3965" 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_2</span><span class="p">,</span> <span class="n" style="color: #333;">B4_2</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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3966
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<pre style="margin: 0;">+<span id="LC3966" 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_3</span><span class="p">,</span> <span class="n" style="color: #333;">B4_3</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">);</span></span>
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3967
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<pre style="margin: 0;">+<span id="LC3967" 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_4</span><span class="p">,</span> <span class="n" style="color: #333;">B4_4</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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3968
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<pre style="margin: 0;">+<span id="LC3968" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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3969
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<pre style="margin: 0;">+<span id="LC3969" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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3970
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<pre style="margin: 0;">+<span id="LC3970" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_2</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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3971
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<pre style="margin: 0;">+<span id="LC3971" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_3</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">);</span></span>
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3972
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<pre style="margin: 0;">+<span id="LC3972" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_4</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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3973
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<pre style="margin: 0;">+<span id="LC3973" 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="mi" style="color: #099;">10</span><span class="p">);</span></span>
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3974
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<pre style="margin: 0;">+<span id="LC3974" 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_1</span><span class="p">,</span> <span class="n" style="color: #333;">B4_1</span><span class="p">,</span> <span class="mi" style="color: #099;">12</span><span class="p">);</span></span>
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3975
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<pre style="margin: 0;">+<span id="LC3975" 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_2</span><span class="p">,</span> <span class="n" style="color: #333;">B4_2</span><span class="p">,</span> <span class="mi" style="color: #099;">14</span><span class="p">);</span></span>
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3976
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<pre style="margin: 0;">+<span id="LC3976" 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_3</span><span class="p">,</span> <span class="n" style="color: #333;">B4_3</span><span class="p">,</span> <span class="mi" style="color: #099;">16</span><span class="p">);</span></span>
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3977
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<pre style="margin: 0;">+<span id="LC3977" 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_4</span><span class="p">,</span> <span class="n" style="color: #333;">B4_4</span><span class="p">,</span> <span class="mi" style="color: #099;">18</span><span class="p">);</span></span>
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3978
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<pre style="margin: 0;">+<span id="LC3978" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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3979
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<pre style="margin: 0;">+<span id="LC3979" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_1</span><span class="p">,</span> <span class="mi" style="color: #099;">12</span><span class="p">);</span></span>
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3980
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<pre style="margin: 0;">+<span id="LC3980" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_2</span><span class="p">,</span> <span class="mi" style="color: #099;">14</span><span class="p">);</span></span>
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3981
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<pre style="margin: 0;">+<span id="LC3981" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_3</span><span class="p">,</span> <span class="mi" style="color: #099;">16</span><span class="p">);</span></span>
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3982
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<pre style="margin: 0;">+<span id="LC3982" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_4</span><span class="p">,</span> <span class="mi" style="color: #099;">18</span><span class="p">);</span></span>
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3983
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<pre style="margin: 0;">+<span id="LC3983" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//}</span></span>
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3984
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<pre style="margin: 0;">+<span id="LC3984" class="line" lang="cpp"> <span class="p">}</span></span>
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3985
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<pre style="margin: 0;">+<span id="LC3985" class="line" lang="cpp"> <span class="p">}</span></span>
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3986
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<pre style="margin: 0;">+<span id="LC3986" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span></span>
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3987
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<pre style="margin: 0;">+<span id="LC3987" 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;">0</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;">vDim</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="n" style="color: #333;">row_offset</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>
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3988
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<pre style="margin: 0;">+<span id="LC3988" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3989
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<pre style="margin: 0;">+<span id="LC3989" 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;">vDim</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;">ti</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">col_offset</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>
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3990
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<pre style="margin: 0;">+<span id="LC3990" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">A4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdupq_n_f64</span><span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]);</span></span>
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3991
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<pre style="margin: 0;">+<span id="LC3991" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>
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3992
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<pre style="margin: 0;">+<span id="LC3992" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop vectorize(enable)</span></span>
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3993
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<pre style="margin: 0;">+<span id="LC3993" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop interleave(enable)</span></span>
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3994
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<pre style="margin: 0;">+<span id="LC3994" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop unroll(enable)</span></span>
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3995
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<pre style="margin: 0;">+<span id="LC3995" 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>
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3996
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<pre style="margin: 0;">+<span id="LC3996" 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>
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3997
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<pre style="margin: 0;">+<span id="LC3997" 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>
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3998
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<pre style="margin: 0;">+<span id="LC3998" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>
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3999
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<pre style="margin: 0;">+<span id="LC3999" class="line" lang="cpp"> <span class="p">}</span></span>
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4000
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<pre style="margin: 0;">+<span id="LC4000" class="line" lang="cpp"> <span class="p">}</span></span>
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4001
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<pre style="margin: 0;">+<span id="LC4001" class="line" lang="cpp"> <span class="p">}</span></span>
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4002
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<pre style="margin: 0;">+<span id="LC4002" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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3872
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4003
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<pre style="margin: 0;"> <span id="LC4003" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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3873
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4004
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<pre style="margin: 0;"> <span id="LC4004" class="line" lang="cpp"> <span class="n" style="color: #333;">memset</span> <span class="p">(</span><span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">*</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>
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3874
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4005
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<pre style="margin: 0;"> <span id="LC4005" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3970" style="width: 35px; color: rgba(0,0,0,0.3); 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="4101" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3970,7 +4101,6 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix const& secondArg) const</td>
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3970
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4101
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<pre style="margin: 0;"> <span id="LC4101" class="line" lang="cpp"></span>
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3971
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4102
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<pre style="margin: 0;"> <span id="LC4102" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dimm4</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">60UL</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// codons</span></span>
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3972
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4103
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<pre style="margin: 0;"> <span id="LC4103" class="line" lang="cpp"> </span>
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3973
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<pre style="margin: 0;">-<span id="LC3973" class="line" lang="cpp"> </span>
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3974
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4104
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<pre style="margin: 0;"> <span id="LC4104" 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;">0</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;">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="n" style="color: #333;">row_offset</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>
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3975
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4105
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<pre style="margin: 0;"> <span id="LC4105" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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3976
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4106
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<pre style="margin: 0;"> <span id="LC4106" 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;">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="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">col_offset</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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4147" style="width: 35px; color: rgba(0,0,0,0.3); 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="4277" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4147,7 +4277,116 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix const& secondArg) const</td>
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4147
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4277
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<pre style="margin: 0;"> <span id="LC4277" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="4148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4148
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4278
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<pre style="margin: 0;"> <span id="LC4278" class="line" lang="cpp"> <span class="p">}</span></span>
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4149
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4279
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<pre style="margin: 0;"> <span id="LC4279" class="line" lang="cpp"> <span class="p">}</span></span>
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4150
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<pre style="margin: 0;">-<span id="LC4150" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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4280
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<pre style="margin: 0;">+<span id="LC4280" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#elif _SLKP_USE_ARM_NEON</span></span>
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4281
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<pre style="margin: 0;">+<span id="LC4281" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">ti</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">,</span></span>
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4282
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<pre style="margin: 0;">+<span id="LC4282" class="line" lang="cpp"> <span class="n" style="color: #333;">row_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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4283
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<pre style="margin: 0;">+<span id="LC4283" class="line" lang="cpp"></span>
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4284
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<pre style="margin: 0;">+<span id="LC4284" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dimm4</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">60UL</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// codons</span></span>
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4285
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<pre style="margin: 0;">+<span id="LC4285" class="line" lang="cpp"> </span>
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4286
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<pre style="margin: 0;">+<span id="LC4286" class="line" lang="cpp"> </span>
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4287
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<pre style="margin: 0;">+<span id="LC4287" 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;">0</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;">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="n" style="color: #333;">row_offset</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>
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4288
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<pre style="margin: 0;">+<span id="LC4288" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4289
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<pre style="margin: 0;">+<span id="LC4289" 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;">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="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">col_offset</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>
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<td class="diff-line-num new new_line" data-linenumber="4290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4290
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<pre style="margin: 0;">+<span id="LC4290" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">A4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdupq_n_f64</span><span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]);</span></span>
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4291
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<pre style="margin: 0;">+<span id="LC4291" class="line" lang="cpp"> </span>
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4292
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<pre style="margin: 0;">+<span id="LC4292" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">D4_1</span><span class="p">,</span> <span class="n" style="color: #333;">D4_2</span><span class="p">,</span> <span class="n" style="color: #333;">D4_3</span><span class="p">,</span> <span class="n" style="color: #333;">D4_4</span><span class="p">;</span></span>
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4293
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<pre style="margin: 0;">+<span id="LC4293" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">B4_1</span><span class="p">,</span> <span class="n" style="color: #333;">B4_2</span><span class="p">,</span> <span class="n" style="color: #333;">B4_3</span><span class="p">,</span> <span class="n" style="color: #333;">B4_4</span><span class="p">;</span></span>
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4294
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<pre style="margin: 0;">+<span id="LC4294" class="line" lang="cpp"> </span>
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4295
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<pre style="margin: 0;">+<span id="LC4295" 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_1</span><span class="p">,</span><span class="n" style="color: #333;">B4_1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4296
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<pre style="margin: 0;">+<span id="LC4296" 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_2</span><span class="p">,</span><span class="n" style="color: #333;">B4_2</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4297
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<pre style="margin: 0;">+<span id="LC4297" 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_3</span><span class="p">,</span><span class="n" style="color: #333;">B4_3</span><span class="p">,</span><span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4298
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<pre style="margin: 0;">+<span id="LC4298" 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_4</span><span class="p">,</span><span class="n" style="color: #333;">B4_4</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">);</span></span>
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4299
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<pre style="margin: 0;">+<span id="LC4299" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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4300
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<pre style="margin: 0;">+<span id="LC4300" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_2</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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4301
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<pre style="margin: 0;">+<span id="LC4301" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_3</span><span class="p">,</span><span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4302
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<pre style="margin: 0;">+<span id="LC4302" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_4</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4303
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<pre style="margin: 0;">+<span id="LC4303" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="4304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4304
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<pre style="margin: 0;">+<span id="LC4304" 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_1</span><span class="p">,</span><span class="n" style="color: #333;">B4_1</span><span class="p">,</span><span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4305
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<pre style="margin: 0;">+<span id="LC4305" 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_2</span><span class="p">,</span><span class="n" style="color: #333;">B4_2</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4306
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<pre style="margin: 0;">+<span id="LC4306" 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_3</span><span class="p">,</span><span class="n" style="color: #333;">B4_3</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4307
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<pre style="margin: 0;">+<span id="LC4307" 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_4</span><span class="p">,</span><span class="n" style="color: #333;">B4_4</span><span class="p">,</span><span class="mi" style="color: #099;">14</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4308
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<pre style="margin: 0;">+<span id="LC4308" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_1</span><span class="p">,</span><span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4309
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<pre style="margin: 0;">+<span id="LC4309" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_2</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4310
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<pre style="margin: 0;">+<span id="LC4310" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_3</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4311
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<pre style="margin: 0;">+<span id="LC4311" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_4</span><span class="p">,</span><span class="mi" style="color: #099;">14</span><span class="p">);</span></span>
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4312
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<pre style="margin: 0;">+<span id="LC4312" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="4313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4313
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<pre style="margin: 0;">+<span id="LC4313" 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_1</span><span class="p">,</span><span class="n" style="color: #333;">B4_1</span><span class="p">,</span><span class="mi" style="color: #099;">16</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4314
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<pre style="margin: 0;">+<span id="LC4314" 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_2</span><span class="p">,</span><span class="n" style="color: #333;">B4_2</span><span class="p">,</span><span class="mi" style="color: #099;">18</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4315
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<pre style="margin: 0;">+<span id="LC4315" 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_3</span><span class="p">,</span><span class="n" style="color: #333;">B4_3</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4316
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<pre style="margin: 0;">+<span id="LC4316" 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_4</span><span class="p">,</span><span class="n" style="color: #333;">B4_4</span><span class="p">,</span><span class="mi" style="color: #099;">22</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4317
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<pre style="margin: 0;">+<span id="LC4317" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_1</span><span class="p">,</span><span class="mi" style="color: #099;">16</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4318
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<pre style="margin: 0;">+<span id="LC4318" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_2</span><span class="p">,</span><span class="mi" style="color: #099;">18</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="4319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4319
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<pre style="margin: 0;">+<span id="LC4319" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_3</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="4320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4320
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<pre style="margin: 0;">+<span id="LC4320" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_4</span><span class="p">,</span><span class="mi" style="color: #099;">22</span><span class="p">);</span></span>
</pre>
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4321
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<pre style="margin: 0;">+<span id="LC4321" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="4322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4322
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<pre style="margin: 0;">+<span id="LC4322" 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_1</span><span class="p">,</span><span class="n" style="color: #333;">B4_1</span><span class="p">,</span><span class="mi" style="color: #099;">24</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4323
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<pre style="margin: 0;">+<span id="LC4323" 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_2</span><span class="p">,</span><span class="n" style="color: #333;">B4_2</span><span class="p">,</span><span class="mi" style="color: #099;">26</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4324
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<pre style="margin: 0;">+<span id="LC4324" 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_3</span><span class="p">,</span><span class="n" style="color: #333;">B4_3</span><span class="p">,</span><span class="mi" style="color: #099;">28</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4325
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<pre style="margin: 0;">+<span id="LC4325" 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_4</span><span class="p">,</span><span class="n" style="color: #333;">B4_4</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4326
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<pre style="margin: 0;">+<span id="LC4326" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_1</span><span class="p">,</span><span class="mi" style="color: #099;">24</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4327
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<pre style="margin: 0;">+<span id="LC4327" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_2</span><span class="p">,</span><span class="mi" style="color: #099;">26</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4328
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<pre style="margin: 0;">+<span id="LC4328" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_3</span><span class="p">,</span><span class="mi" style="color: #099;">28</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4329
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<pre style="margin: 0;">+<span id="LC4329" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_4</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="p">);</span></span>
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4330
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<pre style="margin: 0;">+<span id="LC4330" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="4331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4331
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<pre style="margin: 0;">+<span id="LC4331" 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_1</span><span class="p">,</span><span class="n" style="color: #333;">B4_1</span><span class="p">,</span><span class="mi" style="color: #099;">32</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4332
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<pre style="margin: 0;">+<span id="LC4332" 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_2</span><span class="p">,</span><span class="n" style="color: #333;">B4_2</span><span class="p">,</span><span class="mi" style="color: #099;">34</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4333
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<pre style="margin: 0;">+<span id="LC4333" 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_3</span><span class="p">,</span><span class="n" style="color: #333;">B4_3</span><span class="p">,</span><span class="mi" style="color: #099;">36</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4334
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<pre style="margin: 0;">+<span id="LC4334" 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_4</span><span class="p">,</span><span class="n" style="color: #333;">B4_4</span><span class="p">,</span><span class="mi" style="color: #099;">38</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4335
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<pre style="margin: 0;">+<span id="LC4335" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_1</span><span class="p">,</span><span class="mi" style="color: #099;">32</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4336
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<pre style="margin: 0;">+<span id="LC4336" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_2</span><span class="p">,</span><span class="mi" style="color: #099;">34</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4337
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<pre style="margin: 0;">+<span id="LC4337" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_3</span><span class="p">,</span><span class="mi" style="color: #099;">36</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4338
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<pre style="margin: 0;">+<span id="LC4338" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_4</span><span class="p">,</span><span class="mi" style="color: #099;">38</span><span class="p">);</span></span>
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4339
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<pre style="margin: 0;">+<span id="LC4339" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="4340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4340
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<pre style="margin: 0;">+<span id="LC4340" 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_1</span><span class="p">,</span><span class="n" style="color: #333;">B4_1</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4341
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<pre style="margin: 0;">+<span id="LC4341" 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_2</span><span class="p">,</span><span class="n" style="color: #333;">B4_2</span><span class="p">,</span><span class="mi" style="color: #099;">42</span><span class="p">);</span></span>
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4342
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<pre style="margin: 0;">+<span id="LC4342" 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_3</span><span class="p">,</span><span class="n" style="color: #333;">B4_3</span><span class="p">,</span><span class="mi" style="color: #099;">44</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4343
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<pre style="margin: 0;">+<span id="LC4343" 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_4</span><span class="p">,</span><span class="n" style="color: #333;">B4_4</span><span class="p">,</span><span class="mi" style="color: #099;">46</span><span class="p">);</span></span>
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4344
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<pre style="margin: 0;">+<span id="LC4344" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_1</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="p">);</span></span>
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4345
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<pre style="margin: 0;">+<span id="LC4345" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_2</span><span class="p">,</span><span class="mi" style="color: #099;">42</span><span class="p">);</span></span>
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4346
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<pre style="margin: 0;">+<span id="LC4346" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_3</span><span class="p">,</span><span class="mi" style="color: #099;">44</span><span class="p">);</span></span>
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4347
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<pre style="margin: 0;">+<span id="LC4347" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_4</span><span class="p">,</span><span class="mi" style="color: #099;">46</span><span class="p">);</span></span>
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4348
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<pre style="margin: 0;">+<span id="LC4348" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="4349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4349
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<pre style="margin: 0;">+<span id="LC4349" 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_1</span><span class="p">,</span><span class="n" style="color: #333;">B4_1</span><span class="p">,</span><span class="mi" style="color: #099;">48</span><span class="p">);</span></span>
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4350
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<pre style="margin: 0;">+<span id="LC4350" 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_2</span><span class="p">,</span><span class="n" style="color: #333;">B4_2</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="p">);</span></span>
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4351
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<pre style="margin: 0;">+<span id="LC4351" 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_3</span><span class="p">,</span><span class="n" style="color: #333;">B4_3</span><span class="p">,</span><span class="mi" style="color: #099;">52</span><span class="p">);</span></span>
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4352
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<pre style="margin: 0;">+<span id="LC4352" 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_4</span><span class="p">,</span><span class="n" style="color: #333;">B4_4</span><span class="p">,</span><span class="mi" style="color: #099;">54</span><span class="p">);</span></span>
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4353
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<pre style="margin: 0;">+<span id="LC4353" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_1</span><span class="p">,</span><span class="mi" style="color: #099;">48</span><span class="p">);</span></span>
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4354
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<pre style="margin: 0;">+<span id="LC4354" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_2</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="p">);</span></span>
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4355
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<pre style="margin: 0;">+<span id="LC4355" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_3</span><span class="p">,</span><span class="mi" style="color: #099;">52</span><span class="p">);</span></span>
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4356
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<pre style="margin: 0;">+<span id="LC4356" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_4</span><span class="p">,</span><span class="mi" style="color: #099;">54</span><span class="p">);</span></span>
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4357
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<pre style="margin: 0;">+<span id="LC4357" class="line" lang="cpp"> </span>
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4358
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<pre style="margin: 0;">+<span id="LC4358" 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_1</span><span class="p">,</span><span class="n" style="color: #333;">B4_1</span><span class="p">,</span><span class="mi" style="color: #099;">56</span><span class="p">);</span></span>
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4359
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<pre style="margin: 0;">+<span id="LC4359" 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_2</span><span class="p">,</span><span class="n" style="color: #333;">B4_2</span><span class="p">,</span><span class="mi" style="color: #099;">58</span><span class="p">);</span></span>
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4360
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<pre style="margin: 0;">+<span id="LC4360" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_1</span><span class="p">,</span><span class="mi" style="color: #099;">56</span><span class="p">);</span></span>
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4361
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<pre style="margin: 0;">+<span id="LC4361" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_2</span><span class="p">,</span><span class="mi" style="color: #099;">58</span><span class="p">);</span></span>
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4362
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<pre style="margin: 0;">+<span id="LC4362" class="line" lang="cpp"> </span>
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4363
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<pre style="margin: 0;">+<span id="LC4363" 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;">dimm4</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="p">)</span> <span class="p">{</span></span>
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4364
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<pre style="margin: 0;">+<span id="LC4364" class="line" lang="cpp"> <span class="n" style="color: #333;">dest</span><span class="p">[</span><span class="n" style="color: #333;">row_offset</span> <span class="o" style="font-weight: 600;">+</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;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">secondArg</span><span class="p">.</span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">col_offset</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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4365
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<pre style="margin: 0;">+<span id="LC4365" class="line" lang="cpp"> <span class="p">}</span></span>
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4366
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<pre style="margin: 0;">+<span id="LC4366" class="line" lang="cpp"> <span class="p">}</span></span>
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4367
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<pre style="margin: 0;">+<span id="LC4367" class="line" lang="cpp"> <span class="p">}</span></span>
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4368
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<pre style="margin: 0;">+<span id="LC4368" 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;">// something else</span></span>
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4369
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<pre style="margin: 0;">+<span id="LC4369" 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;">0</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;">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="n" style="color: #333;">row_offset</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>
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4370
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<pre style="margin: 0;">+<span id="LC4370" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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4371
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<pre style="margin: 0;">+<span id="LC4371" 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;">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="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">col_offset</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>
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4372
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<pre style="margin: 0;">+<span id="LC4372" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">A4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdupq_n_f64</span><span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]);</span></span>
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4373
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<pre style="margin: 0;">+<span id="LC4373" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>
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4374
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<pre style="margin: 0;">+<span id="LC4374" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop vectorize(enable)</span></span>
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4375
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<pre style="margin: 0;">+<span id="LC4375" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop interleave(enable)</span></span>
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4376
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<pre style="margin: 0;">+<span id="LC4376" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop unroll(enable)</span></span>
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4377
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<pre style="margin: 0;">+<span id="LC4377" 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>
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4378
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<pre style="margin: 0;">+<span id="LC4378" 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>
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4379
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<pre style="margin: 0;">+<span id="LC4379" 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>
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4380
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<pre style="margin: 0;">+<span id="LC4380" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>
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4381
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<pre style="margin: 0;">+<span id="LC4381" class="line" lang="cpp"> <span class="p">}</span></span>
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4382
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<pre style="margin: 0;">+<span id="LC4382" class="line" lang="cpp"> </span>
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4383
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<pre style="margin: 0;">+<span id="LC4383" 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;">dimm4</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="p">)</span> <span class="p">{</span></span>
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4384
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<pre style="margin: 0;">+<span id="LC4384" class="line" lang="cpp"> <span class="n" style="color: #333;">dest</span><span class="p">[</span><span class="n" style="color: #333;">row_offset</span> <span class="o" style="font-weight: 600;">+</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;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">secondArg</span><span class="p">.</span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">col_offset</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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4385
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<pre style="margin: 0;">+<span id="LC4385" class="line" lang="cpp"> <span class="p">}</span></span>
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4386
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<pre style="margin: 0;">+<span id="LC4386" class="line" lang="cpp"> <span class="p">}</span></span>
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4387
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<pre style="margin: 0;">+<span id="LC4387" class="line" lang="cpp"> <span class="p">}</span></span>
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4388
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<pre style="margin: 0;">+<span id="LC4388" class="line" lang="cpp"> <span class="p">}</span></span>
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4389
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<pre style="margin: 0;">+<span id="LC4389" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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4151
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4390
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<pre style="margin: 0;"> <span id="LC4390" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span></span>
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4152
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4391
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<pre style="margin: 0;"> <span id="LC4391" class="line" lang="cpp"> <span class="n" style="color: #333;">column_shift2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">secondArg</span><span class="p">.</span><span class="n" style="color: #333;">vDim</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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4153
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4392
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<pre style="margin: 0;"> <span id="LC4392" class="line" lang="cpp"> <span class="n" style="color: #333;">column_shift3</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">secondArg</span><span class="p">.</span><span class="n" style="color: #333;">vDim</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">secondArg</span><span class="p">.</span><span class="n" style="color: #333;">vDim</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4185" style="width: 35px; color: rgba(0,0,0,0.3); 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="4424" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4185,7 +4424,7 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix const& secondArg) const</td>
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4185
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4424
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<pre style="margin: 0;"> <span id="LC4424" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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4186
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4425
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<pre style="margin: 0;"> <span id="LC4425" class="line" lang="cpp"> <span class="p">}</span></span>
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4187
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4426
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<pre style="margin: 0;"> <span id="LC4426" class="line" lang="cpp"> </span>
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4188
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<pre style="margin: 0;">-<span id="LC4188" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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4427
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<pre style="margin: 0;">+<span id="LC4427" class="line" lang="cpp"><span class="idiff left right"> </span><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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4189
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4428
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<pre style="margin: 0;"> <span id="LC4428" class="line" lang="cpp"> <span class="n" style="color: #333;">secondArg</span><span class="p">.</span><span class="n" style="color: #333;">Transpose</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="4190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4190
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4429
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<pre style="margin: 0;"> <span id="LC4429" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">hDim</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="n" style="color: #333;">row</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>
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4191
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4430
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<pre style="margin: 0;"> <span id="LC4430" 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;">j</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">hDim</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4340" style="width: 35px; color: rgba(0,0,0,0.3); 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="4579" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4340,7 +4579,19 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix const& secondArg) const</td>
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4340
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4579
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<pre style="margin: 0;"> <span id="LC4579" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">16</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">24</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">28</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC4580" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">32</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">36</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">40</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">44</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC4581" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">48</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">52</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">56</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC4582" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#elif _SLKP_USE_ARM_NEON</span></span>
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4583
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<pre style="margin: 0;">+<span id="LC4583" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">value_op</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdupq_n_f64</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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4584
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<pre style="margin: 0;">+<span id="LC4584" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define CELL_OP(x) vst1q_f64 (res+x, vfmaq_f64 (vld1q_f64(res+x), value_op, vld1q_f64 (secArg+x)))</span></span>
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<pre style="margin: 0;"> <span id="LC4585" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC4586" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC4587" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">6</span><span class="p">);</span></span>
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4588
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<pre style="margin: 0;">+<span id="LC4588" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">8</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">12</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">14</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC4589" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">16</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">18</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">22</span><span class="p">);</span></span>
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4590
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<pre style="margin: 0;">+<span id="LC4590" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">24</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">26</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">28</span><span class="p">);</span></span>
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4591
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<pre style="margin: 0;">+<span id="LC4591" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">30</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">32</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">34</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">36</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">38</span><span class="p">);</span></span>
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4592
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<pre style="margin: 0;">+<span id="LC4592" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">40</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">42</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">44</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">46</span><span class="p">);</span></span>
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4593
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<pre style="margin: 0;">+<span id="LC4593" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">48</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">50</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">52</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">54</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC4594" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">56</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">58</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC4595" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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4596
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<pre style="margin: 0;"> <span id="LC4596" 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="mi" style="color: #099;">60UL</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">4UL</span><span class="p">)</span> <span class="p">{</span></span>
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4597
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<pre style="margin: 0;"> <span id="LC4597" class="line" lang="cpp"> <span class="n" style="color: #333;">res</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="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">secArg</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4359,6 +4610,7 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix const& secondArg) const</td>
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4359
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4610
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<pre style="margin: 0;"> <span id="LC4610" class="line" lang="cpp"> </span>
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4360
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4611
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<pre style="margin: 0;"> <span id="LC4611" class="line" lang="cpp"> </span>
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4361
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4612
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<pre style="margin: 0;"> <span id="LC4612" 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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4613
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<pre style="margin: 0;">+<span id="LC4613" class="line" lang="cpp"></span>
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4362
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4614
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<pre style="margin: 0;"> <span id="LC4614" 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="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;">lDim</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 class="c1" style="color: #998; font-style: italic;">// loop over entries in the sparse matrix</span></span>
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4363
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4615
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<pre style="margin: 0;"> <span id="LC4615" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theIndex</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>
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4364
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4616
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<pre style="margin: 0;"> <span id="LC4616" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0L</span><span class="p">)</span> <span class="p">{</span></span>
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<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="4632" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4380,13 +4632,26 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix const& secondArg) const</td>
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4380
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4632
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<pre style="margin: 0;"> <span id="LC4632" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">16</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">24</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">28</span><span class="p">);</span></span>
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4381
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4633
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<pre style="margin: 0;"> <span id="LC4633" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">32</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">36</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">40</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">44</span><span class="p">);</span></span>
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4382
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4634
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<pre style="margin: 0;"> <span id="LC4634" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">48</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">52</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">56</span><span class="p">);</span></span>
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4635
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<pre style="margin: 0;">+<span id="LC4635" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#elif _SLKP_USE_ARM_NEON</span></span>
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4636
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<pre style="margin: 0;">+<span id="LC4636" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">value_op</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdupq_n_f64</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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4637
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<pre style="margin: 0;">+<span id="LC4637" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define CELL_OP(x) vst1q_f64 (res+x, vfmaq_f64 (vld1q_f64(res+x), value_op, vld1q_f64 (secArg+x)))</span></span>
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4638
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<pre style="margin: 0;">+<span id="LC4638" class="line" lang="cpp"></span>
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4639
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<pre style="margin: 0;">+<span id="LC4639" class="line" lang="cpp"></span>
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4640
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<pre style="margin: 0;">+<span id="LC4640" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">6</span><span class="p">);</span></span>
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4641
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<pre style="margin: 0;">+<span id="LC4641" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">8</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">12</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">14</span><span class="p">);</span></span>
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4642
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<pre style="margin: 0;">+<span id="LC4642" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">16</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">18</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">22</span><span class="p">);</span></span>
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4643
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<pre style="margin: 0;">+<span id="LC4643" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">24</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">26</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">28</span><span class="p">);</span></span>
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4644
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<pre style="margin: 0;">+<span id="LC4644" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">30</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">32</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">34</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">36</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">38</span><span class="p">);</span></span>
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4645
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<pre style="margin: 0;">+<span id="LC4645" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">40</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">42</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">44</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">46</span><span class="p">);</span></span>
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4646
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<pre style="margin: 0;">+<span id="LC4646" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">48</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">50</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">52</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">54</span><span class="p">);</span></span>
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4647
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<pre style="margin: 0;">+<span id="LC4647" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">56</span><span class="p">);</span><span class="n" style="color: #333;">CELL_OP</span><span class="p">(</span><span class="mi" style="color: #099;">58</span><span class="p">);</span></span>
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4383
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4648
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<pre style="margin: 0;"> <span id="LC4648" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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4384
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<pre style="margin: 0;">-<span id="LC4384" 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="mi" style="color: #099;">60UL</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">4UL</span><span class="p">)</span> <span class="p">{</span></span>
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4385
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<pre style="margin: 0;">-<span id="LC4385" class="line" lang="cpp"> <span class="n" style="color: #333;">res</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="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">secArg</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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4386
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<pre style="margin: 0;">-<span id="LC4386" class="line" lang="cpp"> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">secArg</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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4387
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<pre style="margin: 0;">-<span id="LC4387" class="line" lang="cpp"> <span class="n" style="color: #333;">res</span><span class="p">[</span><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 class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">secArg</span><span class="p">[</span><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>
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4388
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<pre style="margin: 0;">-<span id="LC4388" class="line" lang="cpp"> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">secArg</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">3</span><span class="p">];</span></span>
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4389
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<pre style="margin: 0;">-<span id="LC4389" class="line" lang="cpp"> <span class="p">}</span></span>
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4649
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<pre style="margin: 0;">+<span id="LC4649" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="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="mi" style="color: #099;">60UL</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">4UL</span><span class="p">)</span> <span class="p">{</span></span>
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4650
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<pre style="margin: 0;">+<span id="LC4650" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">res</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="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">secArg</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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4651
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<pre style="margin: 0;">+<span id="LC4651" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">res</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">secArg</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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4652
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<pre style="margin: 0;">+<span id="LC4652" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">res</span><span class="p">[</span><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 class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">secArg</span><span class="p">[</span><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>
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4653
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<pre style="margin: 0;">+<span id="LC4653" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">res</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">secArg</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">3</span><span class="p">];</span></span>
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4654
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<pre style="margin: 0;">+<span id="LC4654" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="p">}</span></span>
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4390
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4655
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<pre style="margin: 0;"> <span id="LC4655" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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4391
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4656
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<pre style="margin: 0;"> <span id="LC4656" class="line" lang="cpp"> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">secArg</span><span class="p">[</span><span class="mi" style="color: #099;">60</span><span class="p">];</span></span>
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4392
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4657
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<pre style="margin: 0;"> <span id="LC4657" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4410" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4410,13 +4675,19 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix const& secondArg) const</td>
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4410
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4675
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<pre style="margin: 0;"> <span id="LC4675" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_AVX_INTRINSICS</span></span>
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4411
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4676
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<pre style="margin: 0;"> <span id="LC4676" class="line" lang="cpp"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">value_op</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_set1_pd</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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4412
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4677
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<pre style="margin: 0;"> <span id="LC4677" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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4678
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<pre style="margin: 0;">+<span id="LC4678" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_ARM_NEON</span></span>
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4679
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<pre style="margin: 0;">+<span id="LC4679" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">value_op</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdupq_n_f64</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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4680
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<pre style="margin: 0;">+<span id="LC4680" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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4413
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4681
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<pre style="margin: 0;"> <span id="LC4681" 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;">loopBound</span><span class="p">;</span> <span class="n" style="color: #333;">i</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>
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4414
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4682
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<pre style="margin: 0;"> <span id="LC4682" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_AVX_INTRINSICS</span></span>
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4415
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<pre style="margin: 0;">-<span id="LC4415" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_FMA3_INTRINSICS</span></span>
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4416
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<pre style="margin: 0;">-<span id="LC4416" class="line" lang="cpp"> <span class="n" style="color: #333;">_mm256_storeu_pd</span> <span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">_mm256_fmadd_pd</span> <span class="p">(</span><span class="n" style="color: #333;">value_op</span><span class="p">,</span> <span class="n" style="color: #333;">_mm256_loadu_pd</span> <span class="p">(</span><span class="n" style="color: #333;">secArg</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">),</span><span class="n" style="color: #333;">_mm256_loadu_pd</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">)));</span></span>
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4417
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<pre style="margin: 0;">-<span id="LC4417" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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4418
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<pre style="margin: 0;">-<span id="LC4418" class="line" lang="cpp"> <span class="n" style="color: #333;">_mm256_storeu_pd</span> <span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">_mm256_add_pd</span> <span class="p">(</span><span class="n" style="color: #333;">_mm256_loadu_pd</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">),</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">value_op</span><span class="p">,</span> <span class="n" style="color: #333;">_mm256_loadu_pd</span> <span class="p">(</span><span class="n" style="color: #333;">secArg</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">))));</span></span>
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4419
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<pre style="margin: 0;">-<span id="LC4419" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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4683
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<pre style="margin: 0;">+<span id="LC4683" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_FMA3_INTRINSICS</span></span>
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4684
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<pre style="margin: 0;">+<span id="LC4684" class="line" lang="cpp"> <span class="n" style="color: #333;">_mm256_storeu_pd</span> <span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">_mm256_fmadd_pd</span> <span class="p">(</span><span class="n" style="color: #333;">value_op</span><span class="p">,</span> <span class="n" style="color: #333;">_mm256_loadu_pd</span> <span class="p">(</span><span class="n" style="color: #333;">secArg</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">),</span><span class="n" style="color: #333;">_mm256_loadu_pd</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">)));</span></span>
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4685
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<pre style="margin: 0;">+<span id="LC4685" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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4686
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<pre style="margin: 0;">+<span id="LC4686" class="line" lang="cpp"> <span class="n" style="color: #333;">_mm256_storeu_pd</span> <span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">_mm256_add_pd</span> <span class="p">(</span><span class="n" style="color: #333;">_mm256_loadu_pd</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">),</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">value_op</span><span class="p">,</span> <span class="n" style="color: #333;">_mm256_loadu_pd</span> <span class="p">(</span><span class="n" style="color: #333;">secArg</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">))));</span></span>
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4687
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<pre style="margin: 0;">+<span id="LC4687" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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4688
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<pre style="margin: 0;">+<span id="LC4688" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#elif defined _SLKP_USE_ARM_NEON</span></span>
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4689
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<pre style="margin: 0;">+<span id="LC4689" class="line" lang="cpp"> <span class="n" style="color: #333;">vst1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">vfmaq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">vld1q_f64</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">),</span> <span class="n" style="color: #333;">value_op</span><span class="p">,</span> <span class="n" style="color: #333;">vld1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">secArg</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">)));</span></span>
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4690
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<pre style="margin: 0;">+<span id="LC4690" class="line" lang="cpp"> <span class="n" style="color: #333;">vst1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">+</span><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 class="n" style="color: #333;">vfmaq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">vld1q_f64</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">+</span><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 class="n" style="color: #333;">value_op</span><span class="p">,</span> <span class="n" style="color: #333;">vld1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">secArg</span><span class="o" style="font-weight: 600;">+</span><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>
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4420
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4691
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<pre style="margin: 0;"> <span id="LC4691" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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4421
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4692
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<pre style="margin: 0;"> <span id="LC4692" class="line" lang="cpp"> <span class="n" style="color: #333;">res</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="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">secArg</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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4422
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4693
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<pre style="margin: 0;"> <span id="LC4693" class="line" lang="cpp"> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">secArg</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4446,6 +4717,9 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix const& secondArg) const</td>
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4446
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4717
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<pre style="margin: 0;"> <span id="LC4717" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_AVX_INTRINSICS</span></span>
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4447
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4718
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<pre style="margin: 0;"> <span id="LC4718" class="line" lang="cpp"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">value_op</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_set1_pd</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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4448
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4719
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<pre style="margin: 0;"> <span id="LC4719" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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4720
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<pre style="margin: 0;">+<span id="LC4720" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_ARM_NEON</span></span>
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4721
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<pre style="margin: 0;">+<span id="LC4721" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">value_op</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdupq_n_f64</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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4722
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<pre style="margin: 0;">+<span id="LC4722" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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4449
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4723
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<pre style="margin: 0;"> <span id="LC4723" class="line" lang="cpp"> </span>
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4450
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4724
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<pre style="margin: 0;"> <span id="LC4724" 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;">loopBound</span><span class="p">;</span> <span class="n" style="color: #333;">i</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>
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4451
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4725
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<pre style="margin: 0;"> <span id="LC4725" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_AVX_INTRINSICS</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">@@ -4454,12 +4728,16 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix const& secondArg) const</td>
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4454
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4728
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<pre style="margin: 0;"> <span id="LC4728" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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4455
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4729
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<pre style="margin: 0;"> <span id="LC4729" class="line" lang="cpp"> <span class="n" style="color: #333;">_mm256_storeu_pd</span> <span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">_mm256_add_pd</span> <span class="p">(</span><span class="n" style="color: #333;">_mm256_loadu_pd</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">),</span> <span class="n" style="color: #333;">_mm256_mul_pd</span><span class="p">(</span><span class="n" style="color: #333;">value_op</span><span class="p">,</span> <span class="n" style="color: #333;">_mm256_loadu_pd</span> <span class="p">(</span><span class="n" style="color: #333;">secArg</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">))));</span></span>
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4456
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4730
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<pre style="margin: 0;"> <span id="LC4730" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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4731
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<pre style="margin: 0;">+<span id="LC4731" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#elif defined _SLKP_USE_ARM_NEON</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4732
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<pre style="margin: 0;">+<span id="LC4732" class="line" lang="cpp"> <span class="n" style="color: #333;">vst1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">vfmaq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">vld1q_f64</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">),</span> <span class="n" style="color: #333;">value_op</span><span class="p">,</span> <span class="n" style="color: #333;">vld1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">secArg</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">)));</span></span>
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4733
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<pre style="margin: 0;">+<span id="LC4733" class="line" lang="cpp"> <span class="n" style="color: #333;">vst1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">+</span><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 class="n" style="color: #333;">vfmaq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">vld1q_f64</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">+</span><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 class="n" style="color: #333;">value_op</span><span class="p">,</span> <span class="n" style="color: #333;">vld1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">secArg</span><span class="o" style="font-weight: 600;">+</span><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>
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4457
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4734
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<pre style="margin: 0;"> <span id="LC4734" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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4458
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4735
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<pre style="margin: 0;"> <span id="LC4735" class="line" lang="cpp"> <span class="n" style="color: #333;">res</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="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">secArg</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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4459
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4736
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<pre style="margin: 0;"> <span id="LC4736" class="line" lang="cpp"> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">secArg</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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4460
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4737
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<pre style="margin: 0;"> <span id="LC4737" class="line" lang="cpp"> <span class="n" style="color: #333;">res</span><span class="p">[</span><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 class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">secArg</span><span class="p">[</span><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>
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4461
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4738
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<pre style="margin: 0;"> <span id="LC4738" class="line" lang="cpp"> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">secArg</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">3</span><span class="p">];</span></span>
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4462
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4739
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<pre style="margin: 0;"> <span id="LC4739" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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4740
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<pre style="margin: 0;">+<span id="LC4740" class="line" lang="cpp"> </span>
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4463
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4741
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<pre style="margin: 0;"> <span id="LC4741" class="line" lang="cpp"> <span class="p">}</span></span>
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4464
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4742
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<pre style="margin: 0;"> <span id="LC4742" 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="n" style="color: #333;">loopBound</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;">vDim</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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4465
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4743
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<pre style="margin: 0;"> <span id="LC4743" class="line" lang="cpp"> <span class="n" style="color: #333;">res</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="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">secArg</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6547,9 +6825,8 @@ hyFloat _Matrix::Sqr (hyFloat* _hprestrict_ stash) {</td>
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6547
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6825
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<pre style="margin: 0;"> <span id="LC6825" class="line" lang="cpp"> <span class="n" style="color: #333;">Swap</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">);</span></span>
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6548
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6826
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<pre style="margin: 0;"> <span id="LC6826" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">DBL_EPSILON</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">1.e4</span><span class="p">;</span></span>
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6549
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6827
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<pre style="margin: 0;"> <span id="LC6827" 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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6550
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<pre style="margin: 0;">-<span id="LC6550" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hDim</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">4</span><span class="p">)</span></span>
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6828
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<pre style="margin: 0;">+<span id="LC6828" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hDim</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">4</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff right">{</span></span></span>
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6551
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6829
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<pre style="margin: 0;"> <span id="LC6829" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// special case for nucleotides</span></span>
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6552
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<pre style="margin: 0;">-<span id="LC6552" class="line" lang="cpp"> <span class="p">{</span></span>
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6553
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6830
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<pre style="margin: 0;"> <span id="LC6830" 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;">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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">16</span><span class="p">;</span> <span class="n" style="color: #333;">i</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>
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6554
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6831
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<pre style="margin: 0;"> <span id="LC6831" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0UL</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">4UL</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="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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6555
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6832
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<pre style="margin: 0;"> <span id="LC6832" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">p1</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;">i</span><span class="p">]</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;">j</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6841" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6564,6 +6841,123 @@ hyFloat _Matrix::Sqr (hyFloat* _hprestrict_ stash) {</td>
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6564
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6841
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<pre style="margin: 0;"> <span id="LC6841" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//vDim - vDim % 4;</span></span>
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6565
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6842
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<pre style="margin: 0;"> <span id="LC6842" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// loop interchange rocks!</span></span>
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6566
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6843
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<pre style="margin: 0;"> <span id="LC6843" class="line" lang="cpp"> </span>
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6844
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<pre style="margin: 0;">+<span id="LC6844" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_ARM_NEON</span></span>
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6845
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<pre style="margin: 0;">+<span id="LC6845" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define DO_GROUP_OP0(X,Y,k) Y = vld1q_f64(theData + col_offset + k); X = vmulq_f64(A4, Y);</span></span>
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6846
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<pre style="margin: 0;">+<span id="LC6846" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define DO_GROUP_OP1(X,Y,k) X = vld1q_f64(dest + row_offset + k); Y = vld1q_f64(theData + col_offset + k); X = vfmaq_f64 (X,A4,Y);</span></span>
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6847
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<pre style="margin: 0;">+<span id="LC6847" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define DO_GROUP_OP2(X,k) vst1q_f64 (dest + row_offset + k,X);</span></span>
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6848
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<pre style="margin: 0;">+<span id="LC6848" class="line" lang="cpp"> </span>
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6849
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<pre style="margin: 0;">+<span id="LC6849" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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6850
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<pre style="margin: 0;">+<span id="LC6850" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_hprestrict_</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stash</span><span class="p">;</span></span>
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6851
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<pre style="margin: 0;">+<span id="LC6851" class="line" lang="cpp"></span>
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6852
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<pre style="margin: 0;">+<span id="LC6852" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">ti</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">,</span></span>
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6853
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<pre style="margin: 0;">+<span id="LC6853" class="line" lang="cpp"> <span class="n" style="color: #333;">row_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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6854
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<pre style="margin: 0;">+<span id="LC6854" class="line" lang="cpp"></span>
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6855
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<pre style="margin: 0;">+<span id="LC6855" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">loopBound</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">60UL</span><span class="p">)</span> <span class="p">{</span></span>
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6856
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<pre style="margin: 0;">+<span id="LC6856" 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;">0</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;">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="n" style="color: #333;">row_offset</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>
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6857
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<pre style="margin: 0;">+<span id="LC6857" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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6858
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<pre style="margin: 0;">+<span id="LC6858" class="line" lang="cpp"> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// row 1</span></span>
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6859
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<pre style="margin: 0;">+<span id="LC6859" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">A4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdupq_n_f64</span> <span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]);</span></span>
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6860
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<pre style="margin: 0;">+<span id="LC6860" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">X1</span><span class="p">,</span> <span class="n" style="color: #333;">X2</span><span class="p">,</span> <span class="n" style="color: #333;">X3</span><span class="p">,</span> <span class="n" style="color: #333;">X4</span><span class="p">,</span></span>
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6861
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<pre style="margin: 0;">+<span id="LC6861" class="line" lang="cpp"> <span class="n" style="color: #333;">Y1</span><span class="p">,</span> <span class="n" style="color: #333;">Y2</span><span class="p">,</span> <span class="n" style="color: #333;">Y3</span><span class="p">,</span> <span class="n" style="color: #333;">Y4</span><span class="p">;</span></span>
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6862
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<pre style="margin: 0;">+<span id="LC6862" class="line" lang="cpp"> </span>
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6863
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<pre style="margin: 0;">+<span id="LC6863" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span> <span class="n" style="color: #333;">Y1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span> <span class="n" style="color: #333;">Y2</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span> <span class="n" style="color: #333;">Y3</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span> <span class="n" style="color: #333;">Y4</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">);</span></span>
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6864
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<pre style="margin: 0;">+<span id="LC6864" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span><span class="mi" style="color: #099;">4</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6865
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<pre style="margin: 0;">+<span id="LC6865" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span> <span class="n" style="color: #333;">Y1</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span> <span class="n" style="color: #333;">Y2</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span> <span class="n" style="color: #333;">Y3</span><span class="p">,</span> <span class="mi" style="color: #099;">12</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span> <span class="n" style="color: #333;">Y4</span><span class="p">,</span> <span class="mi" style="color: #099;">14</span><span class="p">);</span></span>
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6866
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<pre style="margin: 0;">+<span id="LC6866" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span><span class="mi" style="color: #099;">8</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span><span class="mi" style="color: #099;">14</span><span class="p">);</span></span>
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6867
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<pre style="margin: 0;">+<span id="LC6867" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span> <span class="n" style="color: #333;">Y1</span><span class="p">,</span> <span class="mi" style="color: #099;">16</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span> <span class="n" style="color: #333;">Y2</span><span class="p">,</span> <span class="mi" style="color: #099;">18</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span> <span class="n" style="color: #333;">Y3</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span> <span class="n" style="color: #333;">Y4</span><span class="p">,</span> <span class="mi" style="color: #099;">22</span><span class="p">);</span></span>
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6868
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<pre style="margin: 0;">+<span id="LC6868" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span><span class="mi" style="color: #099;">16</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span><span class="mi" style="color: #099;">18</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span><span class="mi" style="color: #099;">22</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6869
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<pre style="margin: 0;">+<span id="LC6869" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span> <span class="n" style="color: #333;">Y1</span><span class="p">,</span> <span class="mi" style="color: #099;">24</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span> <span class="n" style="color: #333;">Y2</span><span class="p">,</span> <span class="mi" style="color: #099;">26</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span> <span class="n" style="color: #333;">Y3</span><span class="p">,</span> <span class="mi" style="color: #099;">28</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span> <span class="n" style="color: #333;">Y4</span><span class="p">,</span> <span class="mi" style="color: #099;">30</span><span class="p">);</span></span>
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6870
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<pre style="margin: 0;">+<span id="LC6870" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span><span class="mi" style="color: #099;">24</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span><span class="mi" style="color: #099;">26</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span><span class="mi" style="color: #099;">28</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="p">);</span></span>
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6871
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<pre style="margin: 0;">+<span id="LC6871" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span> <span class="n" style="color: #333;">Y1</span><span class="p">,</span> <span class="mi" style="color: #099;">32</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span> <span class="n" style="color: #333;">Y2</span><span class="p">,</span> <span class="mi" style="color: #099;">34</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span> <span class="n" style="color: #333;">Y3</span><span class="p">,</span> <span class="mi" style="color: #099;">36</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span> <span class="n" style="color: #333;">Y4</span><span class="p">,</span> <span class="mi" style="color: #099;">38</span><span class="p">);</span></span>
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6872
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<pre style="margin: 0;">+<span id="LC6872" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span><span class="mi" style="color: #099;">32</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span><span class="mi" style="color: #099;">34</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span><span class="mi" style="color: #099;">36</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span><span class="mi" style="color: #099;">38</span><span class="p">);</span></span>
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6873
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<pre style="margin: 0;">+<span id="LC6873" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span> <span class="n" style="color: #333;">Y1</span><span class="p">,</span> <span class="mi" style="color: #099;">40</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span> <span class="n" style="color: #333;">Y2</span><span class="p">,</span> <span class="mi" style="color: #099;">42</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span> <span class="n" style="color: #333;">Y3</span><span class="p">,</span> <span class="mi" style="color: #099;">44</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span> <span class="n" style="color: #333;">Y4</span><span class="p">,</span> <span class="mi" style="color: #099;">46</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6874
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<pre style="margin: 0;">+<span id="LC6874" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span><span class="mi" style="color: #099;">42</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span><span class="mi" style="color: #099;">44</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span><span class="mi" style="color: #099;">46</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6875
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<pre style="margin: 0;">+<span id="LC6875" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span> <span class="n" style="color: #333;">Y1</span><span class="p">,</span> <span class="mi" style="color: #099;">48</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span> <span class="n" style="color: #333;">Y2</span><span class="p">,</span> <span class="mi" style="color: #099;">50</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span> <span class="n" style="color: #333;">Y3</span><span class="p">,</span> <span class="mi" style="color: #099;">52</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span> <span class="n" style="color: #333;">Y4</span><span class="p">,</span> <span class="mi" style="color: #099;">54</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6876
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<pre style="margin: 0;">+<span id="LC6876" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span><span class="mi" style="color: #099;">48</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span><span class="mi" style="color: #099;">52</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span><span class="mi" style="color: #099;">54</span><span class="p">);</span></span>
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6877
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<pre style="margin: 0;">+<span id="LC6877" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span> <span class="n" style="color: #333;">Y1</span><span class="p">,</span> <span class="mi" style="color: #099;">56</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span> <span class="n" style="color: #333;">Y2</span><span class="p">,</span> <span class="mi" style="color: #099;">58</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6878
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<pre style="margin: 0;">+<span id="LC6878" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span><span class="mi" style="color: #099;">56</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span><span class="mi" style="color: #099;">58</span><span class="p">);</span></span>
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6879
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<pre style="margin: 0;">+<span id="LC6879" class="line" lang="cpp"></span>
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6880
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<pre style="margin: 0;">+<span id="LC6880" class="line" lang="cpp"> </span>
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6881
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<pre style="margin: 0;">+<span id="LC6881" 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;">60</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="p">)</span> <span class="p">{</span></span>
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6882
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<pre style="margin: 0;">+<span id="LC6882" class="line" lang="cpp"> <span class="n" style="color: #333;">dest</span><span class="p">[</span><span class="n" style="color: #333;">row_offset</span> <span class="o" style="font-weight: 600;">+</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;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]</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;">k</span><span class="p">];</span></span>
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6883
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<pre style="margin: 0;">+<span id="LC6883" class="line" lang="cpp"> <span class="p">}</span></span>
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6884
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<pre style="margin: 0;">+<span id="LC6884" class="line" lang="cpp"> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vDim</span><span class="p">;</span></span>
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6885
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<pre style="margin: 0;">+<span id="LC6885" class="line" lang="cpp"> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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6886
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<pre style="margin: 0;">+<span id="LC6886" class="line" lang="cpp"> <span class="p">}</span></span>
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6887
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<pre style="margin: 0;">+<span id="LC6887" class="line" lang="cpp"> </span>
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6888
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<pre style="margin: 0;">+<span id="LC6888" 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;">1</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="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">col_offset</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>
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6889
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<pre style="margin: 0;">+<span id="LC6889" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">A4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdupq_n_f64</span> <span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]);</span></span>
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6890
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<pre style="margin: 0;">+<span id="LC6890" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">X1</span><span class="p">,</span> <span class="n" style="color: #333;">X2</span><span class="p">,</span> <span class="n" style="color: #333;">X3</span><span class="p">,</span> <span class="n" style="color: #333;">X4</span><span class="p">,</span></span>
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6891
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<pre style="margin: 0;">+<span id="LC6891" class="line" lang="cpp"> <span class="n" style="color: #333;">Y1</span><span class="p">,</span> <span class="n" style="color: #333;">Y2</span><span class="p">,</span> <span class="n" style="color: #333;">Y3</span><span class="p">,</span> <span class="n" style="color: #333;">Y4</span><span class="p">;</span></span>
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6892
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<pre style="margin: 0;">+<span id="LC6892" class="line" lang="cpp"> </span>
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6893
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<pre style="margin: 0;">+<span id="LC6893" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span> <span class="n" style="color: #333;">Y1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span> <span class="n" style="color: #333;">Y2</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span> <span class="n" style="color: #333;">Y3</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span> <span class="n" style="color: #333;">Y4</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6894
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<pre style="margin: 0;">+<span id="LC6894" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span><span class="mi" style="color: #099;">4</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">);</span></span>
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6895
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<pre style="margin: 0;">+<span id="LC6895" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span> <span class="n" style="color: #333;">Y1</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span> <span class="n" style="color: #333;">Y2</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span> <span class="n" style="color: #333;">Y3</span><span class="p">,</span> <span class="mi" style="color: #099;">12</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span> <span class="n" style="color: #333;">Y4</span><span class="p">,</span> <span class="mi" style="color: #099;">14</span><span class="p">);</span></span>
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6896
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<pre style="margin: 0;">+<span id="LC6896" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span><span class="mi" style="color: #099;">8</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span><span class="mi" style="color: #099;">14</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6897
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<pre style="margin: 0;">+<span id="LC6897" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span> <span class="n" style="color: #333;">Y1</span><span class="p">,</span> <span class="mi" style="color: #099;">16</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span> <span class="n" style="color: #333;">Y2</span><span class="p">,</span> <span class="mi" style="color: #099;">18</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span> <span class="n" style="color: #333;">Y3</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span> <span class="n" style="color: #333;">Y4</span><span class="p">,</span> <span class="mi" style="color: #099;">22</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6898
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<pre style="margin: 0;">+<span id="LC6898" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span><span class="mi" style="color: #099;">16</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span><span class="mi" style="color: #099;">18</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span><span class="mi" style="color: #099;">22</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6899
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<pre style="margin: 0;">+<span id="LC6899" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span> <span class="n" style="color: #333;">Y1</span><span class="p">,</span> <span class="mi" style="color: #099;">24</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span> <span class="n" style="color: #333;">Y2</span><span class="p">,</span> <span class="mi" style="color: #099;">26</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span> <span class="n" style="color: #333;">Y3</span><span class="p">,</span> <span class="mi" style="color: #099;">28</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span> <span class="n" style="color: #333;">Y4</span><span class="p">,</span> <span class="mi" style="color: #099;">30</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6900
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<pre style="margin: 0;">+<span id="LC6900" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span><span class="mi" style="color: #099;">24</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span><span class="mi" style="color: #099;">26</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span><span class="mi" style="color: #099;">28</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6901
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<pre style="margin: 0;">+<span id="LC6901" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span> <span class="n" style="color: #333;">Y1</span><span class="p">,</span> <span class="mi" style="color: #099;">32</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span> <span class="n" style="color: #333;">Y2</span><span class="p">,</span> <span class="mi" style="color: #099;">34</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span> <span class="n" style="color: #333;">Y3</span><span class="p">,</span> <span class="mi" style="color: #099;">36</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span> <span class="n" style="color: #333;">Y4</span><span class="p">,</span> <span class="mi" style="color: #099;">38</span><span class="p">);</span></span>
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6902
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<pre style="margin: 0;">+<span id="LC6902" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span><span class="mi" style="color: #099;">32</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span><span class="mi" style="color: #099;">34</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span><span class="mi" style="color: #099;">36</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span><span class="mi" style="color: #099;">38</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6903
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<pre style="margin: 0;">+<span id="LC6903" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span> <span class="n" style="color: #333;">Y1</span><span class="p">,</span> <span class="mi" style="color: #099;">40</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span> <span class="n" style="color: #333;">Y2</span><span class="p">,</span> <span class="mi" style="color: #099;">42</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span> <span class="n" style="color: #333;">Y3</span><span class="p">,</span> <span class="mi" style="color: #099;">44</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span> <span class="n" style="color: #333;">Y4</span><span class="p">,</span> <span class="mi" style="color: #099;">46</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6904
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<pre style="margin: 0;">+<span id="LC6904" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span><span class="mi" style="color: #099;">42</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span><span class="mi" style="color: #099;">44</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span><span class="mi" style="color: #099;">46</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6905
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<pre style="margin: 0;">+<span id="LC6905" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span> <span class="n" style="color: #333;">Y1</span><span class="p">,</span> <span class="mi" style="color: #099;">48</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span> <span class="n" style="color: #333;">Y2</span><span class="p">,</span> <span class="mi" style="color: #099;">50</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span> <span class="n" style="color: #333;">Y3</span><span class="p">,</span> <span class="mi" style="color: #099;">52</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span> <span class="n" style="color: #333;">Y4</span><span class="p">,</span> <span class="mi" style="color: #099;">54</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6906
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<pre style="margin: 0;">+<span id="LC6906" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span><span class="mi" style="color: #099;">48</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X3</span><span class="p">,</span><span class="mi" style="color: #099;">52</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X4</span><span class="p">,</span><span class="mi" style="color: #099;">54</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6907
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<pre style="margin: 0;">+<span id="LC6907" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span> <span class="n" style="color: #333;">Y1</span><span class="p">,</span> <span class="mi" style="color: #099;">56</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span> <span class="n" style="color: #333;">Y2</span><span class="p">,</span> <span class="mi" style="color: #099;">58</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6908
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<pre style="margin: 0;">+<span id="LC6908" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span><span class="mi" style="color: #099;">56</span><span class="p">);</span> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X2</span><span class="p">,</span><span class="mi" style="color: #099;">58</span><span class="p">);</span></span>
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6909
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<pre style="margin: 0;">+<span id="LC6909" class="line" lang="cpp"> </span>
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6910
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<pre style="margin: 0;">+<span id="LC6910" 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;">60</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="p">)</span> <span class="p">{</span></span>
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6911
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<pre style="margin: 0;">+<span id="LC6911" class="line" lang="cpp"> <span class="n" style="color: #333;">dest</span><span class="p">[</span><span class="n" style="color: #333;">row_offset</span> <span class="o" style="font-weight: 600;">+</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;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]</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;">col_offset</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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6912
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<pre style="margin: 0;">+<span id="LC6912" class="line" lang="cpp"> <span class="p">}</span></span>
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6913
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<pre style="margin: 0;">+<span id="LC6913" class="line" lang="cpp"> <span class="p">}</span></span>
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6914
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<pre style="margin: 0;">+<span id="LC6914" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6915
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<pre style="margin: 0;">+<span id="LC6915" 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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6916
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<pre style="margin: 0;">+<span id="LC6916" 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;">0</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;">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="n" style="color: #333;">row_offset</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>
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6917
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<pre style="margin: 0;">+<span id="LC6917" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6918
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<pre style="margin: 0;">+<span id="LC6918" class="line" lang="cpp"> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// row 1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6919
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<pre style="margin: 0;">+<span id="LC6919" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">A4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdupq_n_f64</span> <span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]);</span></span>
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6920
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<pre style="margin: 0;">+<span id="LC6920" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>
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6921
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<pre style="margin: 0;">+<span id="LC6921" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop vectorize(enable)</span></span>
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6922
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<pre style="margin: 0;">+<span id="LC6922" 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="diff-line-num new new_line" data-linenumber="6923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6923
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<pre style="margin: 0;">+<span id="LC6923" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop unroll(enable)</span></span>
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6924
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<pre style="margin: 0;">+<span id="LC6924" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC ivdep</span></span>
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6925
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<pre style="margin: 0;">+<span id="LC6925" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma ivdep</span></span>
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6926
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<pre style="margin: 0;">+<span id="LC6926" 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>
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<td class="diff-line-num new new_line" data-linenumber="6927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6927
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<pre style="margin: 0;">+<span id="LC6927" 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 class="n" style="color: #333;">X1</span><span class="p">,</span> <span class="n" style="color: #333;">X2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6928
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<pre style="margin: 0;">+<span id="LC6928" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP0</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>
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<td class="diff-line-num new new_line" data-linenumber="6929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6929
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<pre style="margin: 0;">+<span id="LC6929" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span> <span class="n" style="color: #333;">X2</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>
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6930
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<pre style="margin: 0;">+<span id="LC6930" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4</span><span class="p">,</span><span class="n" style="color: #333;">k</span><span class="p">);</span></span>
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6931
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<pre style="margin: 0;">+<span id="LC6931" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X1</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>
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6932
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<pre style="margin: 0;">+<span id="LC6932" class="line" lang="cpp"> <span class="p">}</span></span>
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6933
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<pre style="margin: 0;">+<span id="LC6933" class="line" lang="cpp"> </span>
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6934
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<pre style="margin: 0;">+<span id="LC6934" 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;">loopBound</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="p">)</span> <span class="p">{</span></span>
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6935
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<pre style="margin: 0;">+<span id="LC6935" class="line" lang="cpp"> <span class="n" style="color: #333;">dest</span><span class="p">[</span><span class="n" style="color: #333;">row_offset</span> <span class="o" style="font-weight: 600;">+</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;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]</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;">k</span><span class="p">];</span></span>
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6936
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<pre style="margin: 0;">+<span id="LC6936" class="line" lang="cpp"> <span class="p">}</span></span>
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6937
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<pre style="margin: 0;">+<span id="LC6937" class="line" lang="cpp"> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vDim</span><span class="p">;</span></span>
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6938
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<pre style="margin: 0;">+<span id="LC6938" class="line" lang="cpp"> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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6939
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<pre style="margin: 0;">+<span id="LC6939" class="line" lang="cpp"> <span class="p">}</span></span>
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6940
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<pre style="margin: 0;">+<span id="LC6940" class="line" lang="cpp"> </span>
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6941
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<pre style="margin: 0;">+<span id="LC6941" 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;">1</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="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">col_offset</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>
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6942
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<pre style="margin: 0;">+<span id="LC6942" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">A4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdupq_n_f64</span> <span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]);</span></span>
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6943
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<pre style="margin: 0;">+<span id="LC6943" 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>
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6944
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<pre style="margin: 0;">+<span id="LC6944" 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 class="n" style="color: #333;">X1</span><span class="p">,</span> <span class="n" style="color: #333;">X2</span><span class="p">;</span></span>
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6945
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<pre style="margin: 0;">+<span id="LC6945" 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>
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6946
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<pre style="margin: 0;">+<span id="LC6946" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">X1</span><span class="p">,</span> <span class="n" style="color: #333;">X2</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>
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6947
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<pre style="margin: 0;">+<span id="LC6947" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4</span><span class="p">,</span><span class="n" style="color: #333;">k</span><span class="p">);</span></span>
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6948
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<pre style="margin: 0;">+<span id="LC6948" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">X1</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>
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6949
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<pre style="margin: 0;">+<span id="LC6949" class="line" lang="cpp"> <span class="p">}</span></span>
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6950
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<pre style="margin: 0;">+<span id="LC6950" class="line" lang="cpp"> </span>
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6951
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<pre style="margin: 0;">+<span id="LC6951" 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;">loopBound</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="p">)</span> <span class="p">{</span></span>
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6952
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<pre style="margin: 0;">+<span id="LC6952" class="line" lang="cpp"> <span class="n" style="color: #333;">dest</span><span class="p">[</span><span class="n" style="color: #333;">row_offset</span> <span class="o" style="font-weight: 600;">+</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;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]</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;">col_offset</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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6953
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<pre style="margin: 0;">+<span id="LC6953" class="line" lang="cpp"> <span class="p">}</span></span>
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6954
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<pre style="margin: 0;">+<span id="LC6954" class="line" lang="cpp"> <span class="p">}</span></span>
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6955
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<pre style="margin: 0;">+<span id="LC6955" class="line" lang="cpp"> <span class="p">}</span></span>
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6956
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<pre style="margin: 0;">+<span id="LC6956" class="line" lang="cpp"> <span class="p">}</span></span>
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6957
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<pre style="margin: 0;">+<span id="LC6957" 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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6958
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<pre style="margin: 0;">+<span id="LC6958" class="line" lang="cpp"> </span>
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6959
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<pre style="margin: 0;">+<span id="LC6959" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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6960
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<pre style="margin: 0;">+<span id="LC6960" class="line" lang="cpp"> </span>
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6567
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6961
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<pre style="margin: 0;"> <span id="LC6961" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_AVX_INTRINSICS</span></span>
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6568
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6962
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<pre style="margin: 0;"> <span id="LC6962" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define DO_GROUP_OP0(X,Y,k) Y = _mm256_loadu_pd(theData + col_offset + k); X = _mm256_mul_pd(A4, Y);</span></span>
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6569
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6963
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<pre style="margin: 0;"> <span id="LC6963" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_FMA3_INTRINSICS</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6906" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6906,7 +7300,9 @@ hyFloat _Matrix::Sqr (hyFloat* _hprestrict_ stash) {</td>
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6906
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7300
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<pre style="margin: 0;"> <span id="LC7300" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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6907
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7301
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<pre style="margin: 0;"> <span id="LC7301" class="line" lang="cpp"> <span class="p">}</span></span>
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6908
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7302
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<pre style="margin: 0;"> <span id="LC7302" class="line" lang="cpp"> <span class="p">}</span></span>
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6909
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<pre style="margin: 0;">-<span id="LC6909" class="line" lang="cpp"> </span>
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7303
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<pre style="margin: 0;">+<span id="LC7303" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_ARM_NEON</span></span>
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7304
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<pre style="margin: 0;">+<span id="LC7304" class="line" lang="cpp"> <span class="p">}</span></span>
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7305
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<pre style="margin: 0;">+<span id="LC7305" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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6910
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7306
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<pre style="margin: 0;"> <span id="LC7306" class="line" lang="cpp"> </span>
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6911
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7307
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<pre style="margin: 0;"> <span id="LC7307" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">lDimmod4</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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6912
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7308
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<pre style="margin: 0;"> <span id="LC7308" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">diffs</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span><span class="mf" style="color: #099;">0.0</span><span class="p">};</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/e5c8fd32984d059ec09233aa8f7e5cdb888c538c#9f127084157a2a4e11faf03320db0541dbae15dc"><strong>src/core/tree_evaluator.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -122,6 +122,11 @@ inline double _sse_sum_2 (__m128d const & x) {</td>
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"><span class="p">}</span></span>
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123
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_ARM_NEON</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">_neon_sum_2</span> <span class="p">(</span><span class="n" style="color: #333;">float64x2_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">vgetq_lane_f64</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">vgetq_lane_f64</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"><span class="p">}</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"></span>
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126
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<pre style="margin: 0;"> <span id="LC131" 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>
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127
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132
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<pre style="margin: 0;"> <span id="LC132" 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>
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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="273" style="width: 35px; color: rgba(0,0,0,0.3); 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 +273,40 @@ template<long D, long S> inline void __ll_handle_block10_product_sum_linear (hyF</td>
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268
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp"><span class="p">}</span></span>
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269
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_ARM_NEON</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" 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="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">S</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_block10_product_sum_linear</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="n" style="color: #333;">_hprestrict_</span> <span class="n" style="color: #333;">tT</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;">_hprestrict_</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">float64x2_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lastTotal</span><span class="p">)</span> <span class="p">{</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">T</span> <span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"> <span class="n" style="color: #333;">vld1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="p">),</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="n" style="color: #333;">vld1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">),</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="n" style="color: #333;">vld1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">4</span><span class="p">),</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp"> <span class="n" style="color: #333;">vld1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">6</span><span class="p">),</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp"> <span class="n" style="color: #333;">vld1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">8</span><span class="p">)</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp"> <span class="p">};</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"> </span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">C</span> <span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"> <span class="n" style="color: #333;">vld1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="p">),</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"> <span class="n" style="color: #333;">vld1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">),</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"> <span class="n" style="color: #333;">vld1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">4</span><span class="p">),</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp"> <span class="n" style="color: #333;">vld1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">6</span><span class="p">),</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"> <span class="n" style="color: #333;">vld1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">8</span><span class="p">)</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"> <span class="p">};</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">S</span><span class="p">)</span> <span class="p">{</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vfmaq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">vmulq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">C</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">C</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;">//0+1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vfmaq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">vmulq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">C</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]),</span> <span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">C</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;">//2+3</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vfmaq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">],</span> <span class="n" style="color: #333;">C</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;">//0+1+4</span></span>
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<td class="diff-line-num new new_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vaddq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;">// 0+1+2+3+4</span></span>
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<td class="diff-line-num new new_line" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lastTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vaddq_f64</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lastTotal</span><span class="p">,</span> <span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vfmaq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">vmulq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">C</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">C</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;">//0+1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vfmaq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">vmulq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">C</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]),</span> <span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">C</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;">//2+3</span></span>
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<td class="diff-line-num new new_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vfmaq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">],</span> <span class="n" style="color: #333;">C</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;">//0+1+4</span></span>
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<td class="diff-line-num new new_line" 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">
305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lastTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vaddq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">T</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;">// 0+1+2+3+4</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp"> <span class="p">}</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp"><span class="p">}</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp"></span>
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271
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310
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_AVX_INTRINSICS</span></span>
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272
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<td class="diff-line-num new_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
311
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">D</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="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_block20_product_sum_linear</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="n" style="color: #333;">_hprestrict_</span> <span class="n" style="color: #333;">tT</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;">_hprestrict_</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">__m256d</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lastTotal</span><span class="p">)</span> <span class="p">{</span></span>
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273
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312
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="cpp"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -374,9 +413,9 @@ template<long D, long S> inline __m128d __ll_handle_block10_product_sum (hyFloat</td>
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374
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413
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="cpp"> <span class="n" style="color: #333;">_mm_storeu_pd</span><span class="p">(</span><span class="n" style="color: #333;">parentConditionals</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]);</span></span>
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375
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414
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="cpp"></span>
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376
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415
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="cpp"> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_mm_add_pd</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="cpp"> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_mm_add_pd</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="cpp"> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_mm_add_pd</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="cpp"> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_mm_add_pd</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="cpp"> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_mm_add_pd</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="cpp"> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_mm_add_pd</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">grandTotal</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_pd</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">grandTotal</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">@@ -386,6 +425,57 @@ template<long D, long S> inline __m128d __ll_handle_block10_product_sum (hyFloat</td>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_ARM_NEON</span></span>
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<pre style="margin: 0;">+<span id="LC429" 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="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">S</span><span class="p">></span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">float64x2_t</span> <span class="nf" style="color: #900; font-weight: 600;">__ll_handle_block10_product_sum</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="n" style="color: #333;">_hprestrict_</span> <span class="n" style="color: #333;">transposedMatrix</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;">_hprestrict_</span> <span class="n" style="color: #333;">childVector</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;">_hprestrict_</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">float64x2_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">grandTotal</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">P</span> <span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="cpp"> <span class="n" style="color: #333;">vdupq_n_f64</span><span class="p">(</span><span class="mf" style="color: #099;">0.</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="cpp"> <span class="n" style="color: #333;">vdupq_n_f64</span><span class="p">(</span><span class="mf" style="color: #099;">0.</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="cpp"> <span class="n" style="color: #333;">vdupq_n_f64</span><span class="p">(</span><span class="mf" style="color: #099;">0.</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="cpp"> <span class="n" style="color: #333;">vdupq_n_f64</span><span class="p">(</span><span class="mf" style="color: #099;">0.</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="cpp"> <span class="n" style="color: #333;">vdupq_n_f64</span><span class="p">(</span><span class="mf" style="color: #099;">0.</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="cpp"> <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;">tT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transposedMatrix</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC441" 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;">col_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;">col_idx</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;">col_idx</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">tT</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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<pre style="margin: 0;">+<span id="LC442" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="p">[</span><span class="n" style="color: #333;">col_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">0.</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">C</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdupq_n_f64</span><span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="p">[</span><span class="n" style="color: #333;">col_idx</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="cpp"> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vfmaq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">vld1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="p">),</span> <span class="n" style="color: #333;">C</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="cpp"> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vfmaq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">vld1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">),</span> <span class="n" style="color: #333;">C</span><span class="p">);</span></span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="cpp"> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vfmaq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">vld1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">4</span><span class="p">),</span> <span class="n" style="color: #333;">C</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="cpp"> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vfmaq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">vld1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">6</span><span class="p">),</span> <span class="n" style="color: #333;">C</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cpp"> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vfmaq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">],</span> <span class="n" style="color: #333;">vld1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">8</span><span class="p">),</span> <span class="n" style="color: #333;">C</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="cpp"> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vmulq_f64</span><span class="p">(</span><span class="n" style="color: #333;">vld1q_f64</span><span class="p">(</span><span class="n" style="color: #333;">parentConditionals</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="p">),</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="cpp"> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vmulq_f64</span><span class="p">(</span><span class="n" style="color: #333;">vld1q_f64</span><span class="p">(</span><span class="n" style="color: #333;">parentConditionals</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">),</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="cpp"> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vmulq_f64</span><span class="p">(</span><span class="n" style="color: #333;">vld1q_f64</span><span class="p">(</span><span class="n" style="color: #333;">parentConditionals</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">4</span><span class="p">),</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span></span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="cpp"> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vmulq_f64</span><span class="p">(</span><span class="n" style="color: #333;">vld1q_f64</span><span class="p">(</span><span class="n" style="color: #333;">parentConditionals</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">6</span><span class="p">),</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="cpp"> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vmulq_f64</span><span class="p">(</span><span class="n" style="color: #333;">vld1q_f64</span><span class="p">(</span><span class="n" style="color: #333;">parentConditionals</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">8</span><span class="p">),</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]);</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="cpp"> </span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="cpp"> <span class="n" style="color: #333;">vst1q_f64</span><span class="p">(</span><span class="n" style="color: #333;">parentConditionals</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="p">,</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="cpp"> <span class="n" style="color: #333;">vst1q_f64</span><span class="p">(</span><span class="n" style="color: #333;">parentConditionals</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="cpp"> <span class="n" style="color: #333;">vst1q_f64</span><span class="p">(</span><span class="n" style="color: #333;">parentConditionals</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span></span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="cpp"> <span class="n" style="color: #333;">vst1q_f64</span><span class="p">(</span><span class="n" style="color: #333;">parentConditionals</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="cpp"> <span class="n" style="color: #333;">vst1q_f64</span><span class="p">(</span><span class="n" style="color: #333;">parentConditionals</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]);</span></span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="cpp"></span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="cpp"> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vaddq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="cpp"> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vaddq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="cpp"> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vaddq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="cpp"> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vaddq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span></span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">grandTotal</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vaddq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">grandTotal</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_AVX_INTRINSICS</span></span>
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<pre style="margin: 0;"> <span id="LC480" 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="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">S</span><span class="p">></span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">__m256d</span> <span class="nf" style="color: #900; font-weight: 600;">__ll_handle_block20_product_sum</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="n" style="color: #333;">_hprestrict_</span> <span class="n" style="color: #333;">transposedMatrix</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;">_hprestrict_</span> <span class="n" style="color: #333;">childVector</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;">_hprestrict_</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">__m256d</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">grandTotal</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="cpp"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">P</span> <span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -728,11 +818,12 @@ inline void _handle4x4_pruning_case (double const* childVector, double const* tM</td>
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<pre style="margin: 0;"> <span id="LC818" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC819" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#elif defined _SLKP_USE_AVX_INTRINSICS</span></span>
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<pre style="margin: 0;"> <span id="LC820" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC731" class="line" lang="cpp"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">c3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_set1_pd</span><span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]),</span></span>
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<pre style="margin: 0;">-<span id="LC732" class="line" lang="cpp"> <span class="n" style="color: #333;">c0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_set1_pd</span><span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]),</span></span>
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<pre style="margin: 0;">-<span id="LC733" class="line" lang="cpp"> <span class="n" style="color: #333;">c1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_set1_pd</span><span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span></span>
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<pre style="margin: 0;">-<span id="LC734" class="line" lang="cpp"> <span class="n" style="color: #333;">c2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_set1_pd</span><span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]),</span></span>
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<pre style="margin: 0;">-<span id="LC735" class="line" lang="cpp"> <span class="n" style="color: #333;">t0</span><span class="p">,</span><span class="n" style="color: #333;">t1</span><span class="p">,</span><span class="n" style="color: #333;">t2</span><span class="p">,</span><span class="n" style="color: #333;">t3</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="cpp"> <span class="n" style="color: #333;">__m256d</span></span>
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="cpp"> <span class="n" style="color: #333;">c0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_set1_pd</span><span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]),</span></span>
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="cpp"> <span class="n" style="color: #333;">c1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_set1_pd</span><span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span></span>
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="cpp"> <span class="n" style="color: #333;">c2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_set1_pd</span><span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]),</span></span>
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825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="cpp"> <span class="n" style="color: #333;">c3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_set1_pd</span><span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]),</span></span>
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="cpp"> <span class="n" style="color: #333;">t0</span><span class="p">,</span><span class="n" style="color: #333;">t1</span><span class="p">,</span><span class="n" style="color: #333;">t2</span><span class="p">,</span><span class="n" style="color: #333;">t3</span><span class="p">;</span></span>
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827
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<pre style="margin: 0;"> <span id="LC827" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC828" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">transposed_mx</span><span class="p">)</span> <span class="p">{</span></span>
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738
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829
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<pre style="margin: 0;"> <span id="LC829" class="line" lang="cpp"> <span class="n" style="color: #333;">t0</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">__m256d</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">transposed_mx</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -761,9 +852,38 @@ inline void _handle4x4_pruning_case (double const* childVector, double const* tM</td>
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<pre style="margin: 0;"> <span id="LC852" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC853" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC854" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#elif defined _SLKP_USE_ARM_NEON</span></span>
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">c0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdupq_n_f64</span><span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]),</span></span>
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="cpp"> <span class="n" style="color: #333;">c1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdupq_n_f64</span><span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span></span>
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="cpp"> <span class="n" style="color: #333;">c2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdupq_n_f64</span><span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]),</span></span>
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="cpp"> <span class="n" style="color: #333;">c3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdupq_n_f64</span><span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2x2_t</span> <span class="n" style="color: #333;">t0</span><span class="p">,</span> <span class="n" style="color: #333;">t1</span><span class="p">,</span> <span class="n" style="color: #333;">t2</span><span class="p">,</span> <span class="n" style="color: #333;">t3</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">transposed_mx</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="cpp"> <span class="n" style="color: #333;">t0</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">float64x2x2_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">transposed_mx</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="cpp"> <span class="n" style="color: #333;">t1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">float64x2x2_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">transposed_mx</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="cpp"> <span class="n" style="color: #333;">t2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">float64x2x2_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">transposed_mx</span><span class="p">)[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="cpp"> <span class="n" style="color: #333;">t3</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">float64x2x2_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">transposed_mx</span><span class="p">)[</span><span class="mi" style="color: #099;">3</span><span class="p">];</span></span>
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868
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<pre style="margin: 0;">+<span id="LC868" 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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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="cpp"> <span class="n" style="color: #333;">t0</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">float64x2x2_t</span><span class="p">){</span><span class="n" style="color: #333;">tMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">tMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">],</span><span class="n" style="color: #333;">tMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">],</span><span class="n" style="color: #333;">tMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">12</span><span class="p">]};</span></span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="cpp"> <span class="n" style="color: #333;">t1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">float64x2x2_t</span><span class="p">){</span><span class="n" style="color: #333;">tMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="n" style="color: #333;">tMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">],</span><span class="n" style="color: #333;">tMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">],</span><span class="n" style="color: #333;">tMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">13</span><span class="p">]};</span></span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="cpp"> <span class="n" style="color: #333;">t2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">float64x2x2_t</span><span class="p">){</span><span class="n" style="color: #333;">tMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span><span class="n" style="color: #333;">tMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">],</span><span class="n" style="color: #333;">tMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">],</span><span class="n" style="color: #333;">tMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">14</span><span class="p">]};</span></span>
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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="cpp"> <span class="n" style="color: #333;">t3</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">float64x2x2_t</span><span class="p">){</span><span class="n" style="color: #333;">tMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span><span class="n" style="color: #333;">tMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">],</span><span class="n" style="color: #333;">tMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">],</span><span class="n" style="color: #333;">tMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">15</span><span class="p">]};</span></span>
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="cpp"> <span class="p">}</span></span>
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874
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<pre style="margin: 0;"> <span id="LC874" class="line" lang="cpp"> </span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="cpp"> <span class="n" style="color: #333;">t0</span><span class="p">.</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vfmaq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">vmulq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">c1</span><span class="p">,</span><span class="n" style="color: #333;">t1</span><span class="p">.</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]),</span><span class="n" style="color: #333;">c0</span><span class="p">,</span><span class="n" style="color: #333;">t0</span><span class="p">.</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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876
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="cpp"> <span class="n" style="color: #333;">t0</span><span class="p">.</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vfmaq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">vmulq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">c1</span><span class="p">,</span><span class="n" style="color: #333;">t1</span><span class="p">.</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span><span class="n" style="color: #333;">c0</span><span class="p">,</span><span class="n" style="color: #333;">t0</span><span class="p">.</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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877
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="cpp"> <span class="n" style="color: #333;">t2</span><span class="p">.</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vfmaq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">vmulq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">c3</span><span class="p">,</span><span class="n" style="color: #333;">t3</span><span class="p">.</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]),</span><span class="n" style="color: #333;">c2</span><span class="p">,</span><span class="n" style="color: #333;">t2</span><span class="p">.</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="cpp"> <span class="n" style="color: #333;">t2</span><span class="p">.</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vfmaq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">vmulq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">c3</span><span class="p">,</span><span class="n" style="color: #333;">t3</span><span class="p">.</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span><span class="n" style="color: #333;">c2</span><span class="p">,</span><span class="n" style="color: #333;">t2</span><span class="p">.</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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879
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<pre style="margin: 0;"> <span id="LC879" class="line" lang="cpp"> </span>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="cpp"> <span class="n" style="color: #333;">vst1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="cpp"> <span class="n" style="color: #333;">vmulq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">vld1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">parentConditionals</span><span class="p">),</span> <span class="n" style="color: #333;">vaddq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">t0</span><span class="p">.</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">t2</span><span class="p">.</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])));</span></span>
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882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="cpp"> <span class="n" style="color: #333;">vst1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">parentConditionals</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">vmulq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">vld1q_f64</span> <span class="p">(</span><span class="n" style="color: #333;">parentConditionals</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">),</span> <span class="n" style="color: #333;">vaddq_f64</span> <span class="p">(</span><span class="n" style="color: #333;">t0</span><span class="p">.</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">t2</span><span class="p">.</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])));</span></span>
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="cpp"></span>
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884
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<pre style="margin: 0;"> <span id="LC884" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC887" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 12 multiplications, 16 additions, 3 subtractions</span></span>
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888
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<pre style="margin: 0;"> <span id="LC888" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC889" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*hyFloat t1 = childVector[0] - childVector[3],</span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</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">@@ -836,7 +956,7 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList</td>
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836
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956
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<pre style="margin: 0;"> <span id="LC956" class="line" lang="cpp"> <span class="n" style="color: #333;">siteTo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siteCount</span><span class="p">;</span></span>
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837
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<pre style="margin: 0;"> <span id="LC957" class="line" lang="cpp"> <span class="p">}</span></span>
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958
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<pre style="margin: 0;"> <span id="LC958" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC839" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS</span></span>
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS<span class="idiff left right"> || defined _SLKP_USE_ARM_NEON</span></span></span>
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<pre style="margin: 0;"> <span id="LC960" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tMatrixT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nil</span><span class="p">;</span></span>
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841
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961
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<pre style="margin: 0;"> <span id="LC961" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">alphabetDimension</span><span class="p">)</span> <span class="p">{</span></span>
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962
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<pre style="margin: 0;"> <span id="LC962" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">20</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">@@ -940,6 +1060,16 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList</td>
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940
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1060
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<pre style="margin: 0;"> <span id="LC1060" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">__m256d</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">15</span><span class="p">]}</span></span>
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941
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1061
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<pre style="margin: 0;"> <span id="LC1061" class="line" lang="cpp"> <span class="p">};</span></span>
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942
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1062
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<pre style="margin: 0;"> <span id="LC1062" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">+<span id="LC1063" class="line" lang="cpp"> </span>
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1064
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<pre style="margin: 0;">+<span id="LC1064" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_ARM_NEON</span></span>
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<pre style="margin: 0;">+<span id="LC1065" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2x2_t</span> <span class="n" style="color: #333;">tmatrix_transpose</span> <span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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1066
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<pre style="margin: 0;">+<span id="LC1066" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">float64x2x2_t</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">12</span><span class="p">]},</span></span>
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1067
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<pre style="margin: 0;">+<span id="LC1067" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">float64x2x2_t</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">13</span><span class="p">]},</span></span>
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1068
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<pre style="margin: 0;">+<span id="LC1068" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">float64x2x2_t</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">14</span><span class="p">]},</span></span>
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1069
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<pre style="margin: 0;">+<span id="LC1069" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">float64x2x2_t</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">15</span><span class="p">]}</span></span>
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1070
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<pre style="margin: 0;">+<span id="LC1070" class="line" lang="cpp"> <span class="p">};</span></span>
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1071
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<pre style="margin: 0;">+<span id="LC1071" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">+<span id="LC1072" class="line" lang="cpp"> </span>
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1073
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<pre style="margin: 0;"> <span id="LC1073" 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;">siteID</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;">siteID</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;">siteID</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">4UL</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1074" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_loop_preamble</span></span>
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<pre style="margin: 0;"> <span id="LC1075" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">__ll_handle_conditional_array_initialization</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -949,7 +1079,7 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList</td>
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<pre style="margin: 0;"> <span id="LC1079" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC1080" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC1081" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC952" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if<span class="idiff left right">def _SLKP_USE_AVX_INTRINSICS</span></span></span>
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if<span class="idiff left right"> defined _SLKP_USE_AVX_INTRINSICS or defined _SLKP_USE_ARM_NEON</span></span></span>
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1083
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<pre style="margin: 0;"> <span id="LC1083" class="line" lang="cpp"> <span class="n" style="color: #333;">_handle4x4_pruning_case</span> <span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">tmatrix_transpose</span><span class="p">);</span></span>
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1084
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<pre style="margin: 0;"> <span id="LC1084" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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955
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1085
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<pre style="margin: 0;"> <span id="LC1085" class="line" lang="cpp"> <span class="n" style="color: #333;">_handle4x4_pruning_case</span> <span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">nil</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</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">@@ -968,7 +1098,7 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList</td>
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968
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1098
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<pre style="margin: 0;"> <span id="LC1098" class="line" lang="cpp"> </span>
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969
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1099
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<pre style="margin: 0;"> <span id="LC1099" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// START AMINO-ACID CASE</span></span>
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970
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1100
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<pre style="margin: 0;"> <span id="LC1100" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alphabetDimension</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">20UL</span><span class="p">)</span> <span class="p">{</span></span>
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971
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<pre style="margin: 0;">-<span id="LC971" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1101
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS<span class="idiff left right"> || defined _SLKP_USE_ARM_NEON</span></span></span>
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972
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1102
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<pre style="margin: 0;"> <span id="LC1102" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_matrix_transpose</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrixT</span><span class="p">);</span></span>
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973
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1103
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<pre style="margin: 0;"> <span id="LC1103" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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974
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1104
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<pre style="margin: 0;"> <span id="LC1104" class="line" lang="cpp"> </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1115" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -985,6 +1115,11 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList</td>
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985
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1115
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<pre style="margin: 0;"> <span id="LC1115" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">20</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">nil</span><span class="p">);</span></span>
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986
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1116
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<pre style="margin: 0;"> <span id="LC1116" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">20</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">),</span><span class="n" style="color: #333;">grandTotal</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" 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
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1117
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<pre style="margin: 0;"> <span id="LC1117" 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;">_sse_sum_2</span> <span class="p">(</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1118
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<pre style="margin: 0;">+<span id="LC1118" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#elif defined _SLKP_USE_ARM_NEON</span></span>
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1119
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<pre style="margin: 0;">+<span id="LC1119" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">grandTotal</span></span>
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1120
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<pre style="margin: 0;">+<span id="LC1120" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">20</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">nil</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1121
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<pre style="margin: 0;">+<span id="LC1121" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">20</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">),</span><span class="n" style="color: #333;">grandTotal</span><span class="p">;</span></span>
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1122
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<pre style="margin: 0;">+<span id="LC1122" 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;">_neon_sum_2</span> <span class="p">(</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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988
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1123
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<pre style="margin: 0;"> <span id="LC1123" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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989
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1124
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<pre style="margin: 0;"> <span id="LC1124" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_product_sum_loop</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">20L</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">sum</span><span class="p">);</span></span>
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990
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1125
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<pre style="margin: 0;"> <span id="LC1125" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -999,7 +1134,7 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList</td>
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999
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1134
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<pre style="margin: 0;"> <span id="LC1134" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// END AMINO-ACID CASE</span></span>
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1000
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1135
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<pre style="margin: 0;"> <span id="LC1135" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// START UNIVERSAL CODE</span></span>
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1001
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1136
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<pre style="margin: 0;"> <span id="LC1136" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alphabetDimension</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">60UL</span><span class="p">)</span> <span class="p">{</span></span>
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1002
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<pre style="margin: 0;">-<span id="LC1002" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS</span></span>
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1137
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<pre style="margin: 0;">+<span id="LC1137" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS<span class="idiff left right"> || defined _SLKP_USE_ARM_NEON</span></span></span>
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1003
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1138
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<pre style="margin: 0;"> <span id="LC1138" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_matrix_transpose</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrixT</span><span class="p">);</span></span>
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1004
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1139
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<pre style="margin: 0;"> <span id="LC1139" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1005
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1140
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<pre style="margin: 0;"> <span id="LC1140" 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;">siteID</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;">siteID</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;">siteID</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">60L</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); 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="1160" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1025,6 +1160,15 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList</td>
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1025
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1160
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<pre style="margin: 0;"> <span id="LC1160" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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1026
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1161
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<pre style="margin: 0;"> <span id="LC1161" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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1027
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1162
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<pre style="margin: 0;"> <span id="LC1162" 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;">_sse_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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1163
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<pre style="margin: 0;">+<span id="LC1163" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#elif defined _SLKP_USE_ARM_NEON</span></span>
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1164
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<pre style="margin: 0;">+<span id="LC1164" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">grandTotal</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1165
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<pre style="margin: 0;">+<span id="LC1165" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">nil</span><span class="p">);</span></span>
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1166
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<pre style="margin: 0;">+<span id="LC1166" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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1167
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<pre style="margin: 0;">+<span id="LC1167" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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1168
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<pre style="margin: 0;">+<span id="LC1168" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1169
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<pre style="margin: 0;">+<span id="LC1169" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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1170
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<pre style="margin: 0;">+<span id="LC1170" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1171
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<pre style="margin: 0;">+<span id="LC1171" 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;">_neon_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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1028
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1172
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<pre style="margin: 0;"> <span id="LC1172" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1029
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1173
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<pre style="margin: 0;"> <span id="LC1173" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_product_sum_loop</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60L</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">sum</span><span class="p">);</span></span>
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1030
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1174
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<pre style="margin: 0;"> <span id="LC1174" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1036,7 +1180,7 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList</td>
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1036
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1180
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<pre style="margin: 0;"> <span id="LC1180" class="line" lang="cpp"> <span class="p">}</span></span>
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1037
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1181
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<pre style="margin: 0;"> <span id="LC1181" class="line" lang="cpp"> <span class="p">}</span></span>
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1038
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1182
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<pre style="margin: 0;"> <span id="LC1182" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alphabetDimension</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">61UL</span><span class="p">)</span> <span class="p">{</span></span>
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1039
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<pre style="margin: 0;">-<span id="LC1039" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS</span></span>
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1183
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<pre style="margin: 0;">+<span id="LC1183" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS<span class="idiff left right"> || defined _SLKP_USE_ARM_NEON</span></span></span>
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1040
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1184
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<pre style="margin: 0;"> <span id="LC1184" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_matrix_transpose</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrixT</span><span class="p">);</span></span>
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1041
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1185
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<pre style="margin: 0;"> <span id="LC1185" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1042
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1186
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<pre style="margin: 0;"> <span id="LC1186" 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;">siteID</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;">siteID</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;">siteID</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">61L</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1122" style="width: 35px; color: rgba(0,0,0,0.3); 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="1266" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1122,6 +1266,26 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList</td>
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1122
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1266
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<pre style="margin: 0;"> <span id="LC1266" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">s60</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_sse_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">lastTotal</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="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">60</span><span class="p">];</span></span>
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1123
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1267
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<pre style="margin: 0;"> <span id="LC1267" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</span><span class="p">[</span><span class="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">s60</span><span class="p">;</span></span>
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1124
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1268
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<pre style="margin: 0;"> <span id="LC1268" 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;">_sse_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">grandTotal</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s60</span><span class="p">;</span></span>
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1269
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<pre style="margin: 0;">+<span id="LC1269" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#elif defined _SLKP_USE_ARM_NEON</span></span>
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1270
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<pre style="margin: 0;">+<span id="LC1270" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">grandTotal</span><span class="p">;</span></span>
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1271
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<pre style="margin: 0;">+<span id="LC1271" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">nil</span><span class="p">);</span></span>
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1272
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<pre style="margin: 0;">+<span id="LC1272" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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1273
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<pre style="margin: 0;">+<span id="LC1273" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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1274
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<pre style="margin: 0;">+<span id="LC1274" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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1275
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<pre style="margin: 0;">+<span id="LC1275" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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1276
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<pre style="margin: 0;">+<span id="LC1276" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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1277
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<pre style="margin: 0;">+<span id="LC1277" class="line" lang="cpp"></span>
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1278
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<pre style="margin: 0;">+<span id="LC1278" class="line" lang="cpp"> <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;">tT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tMatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">61</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">60</span><span class="p">;</span></span>
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1279
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<pre style="margin: 0;">+<span id="LC1279" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">lastTotal</span><span class="p">;</span></span>
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1280
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<pre style="margin: 0;">+<span id="LC1280" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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1281
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<pre style="margin: 0;">+<span id="LC1281" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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1282
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<pre style="margin: 0;">+<span id="LC1282" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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1283
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<pre style="margin: 0;">+<span id="LC1283" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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1284
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<pre style="margin: 0;">+<span id="LC1284" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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1285
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<pre style="margin: 0;">+<span id="LC1285" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1286
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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">s60</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_neon_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">lastTotal</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="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">60</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1287
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<pre style="margin: 0;">+<span id="LC1287" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</span><span class="p">[</span><span class="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">s60</span><span class="p">;</span></span>
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1288
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<pre style="margin: 0;">+<span id="LC1288" 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;">_neon_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">grandTotal</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s60</span><span class="p">;</span></span>
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1125
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1289
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<pre style="margin: 0;"> <span id="LC1289" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1126
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1290
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<pre style="margin: 0;"> <span id="LC1290" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_product_sum_loop</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61L</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">sum</span><span class="p">);</span></span>
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1127
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1291
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<pre style="margin: 0;"> <span id="LC1291" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1138" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1138,7 +1302,7 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList</td>
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1138
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1302
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<pre style="margin: 0;"> <span id="LC1302" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_loop_epilogue</span></span>
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1139
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1303
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<pre style="margin: 0;"> <span id="LC1303" class="line" lang="cpp"> <span class="p">}</span></span>
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1140
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1304
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<pre style="margin: 0;"> <span id="LC1304" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alphabetDimension</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">62UL</span><span class="p">)</span> <span class="p">{</span></span>
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1141
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<pre style="margin: 0;">-<span id="LC1141" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS</span></span>
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1305
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<pre style="margin: 0;">+<span id="LC1305" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS<span class="idiff left right"> || defined _SLKP_USE_ARM_NEON</span></span></span>
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1142
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1306
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<pre style="margin: 0;"> <span id="LC1306" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_matrix_transpose</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrixT</span><span class="p">);</span></span>
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1143
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1307
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<pre style="margin: 0;"> <span id="LC1307" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1144
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1308
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<pre style="margin: 0;"> <span id="LC1308" 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;">siteID</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;">siteID</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;">siteID</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">62L</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1370" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1206,6 +1370,40 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList</td>
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1206
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1370
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<pre style="margin: 0;"> <span id="LC1370" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</span><span class="p">[</span><span class="mi" style="color: #099;">61</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">s61</span><span class="p">;</span></span>
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1207
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1371
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<pre style="margin: 0;"> <span id="LC1371" class="line" lang="cpp"></span>
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1208
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1372
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<pre style="margin: 0;"> <span id="LC1372" 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;">_sse_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">grandTotal</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s60</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s61</span><span class="p">;</span></span>
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1373
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<pre style="margin: 0;">+<span id="LC1373" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#elif defined _SLKP_USE_ARM_NEON</span></span>
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1374
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<pre style="margin: 0;">+<span id="LC1374" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">grandTotal</span></span>
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1375
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<pre style="margin: 0;">+<span id="LC1375" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">nil</span><span class="p">);</span></span>
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1376
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<pre style="margin: 0;">+<span id="LC1376" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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1377
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<pre style="margin: 0;">+<span id="LC1377" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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1378
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<pre style="margin: 0;">+<span id="LC1378" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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1379
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<pre style="margin: 0;">+<span id="LC1379" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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1380
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<pre style="margin: 0;">+<span id="LC1380" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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1381
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<pre style="margin: 0;">+<span id="LC1381" class="line" lang="cpp"></span>
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1382
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<pre style="margin: 0;">+<span id="LC1382" class="line" lang="cpp"> <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;">tT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tMatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">62</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">60</span><span class="p">;</span></span>
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1383
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<pre style="margin: 0;">+<span id="LC1383" class="line" lang="cpp"> </span>
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1384
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<pre style="margin: 0;">+<span id="LC1384" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">lastTotal</span><span class="p">;</span></span>
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1385
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<pre style="margin: 0;">+<span id="LC1385" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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1386
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<pre style="margin: 0;">+<span id="LC1386" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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1387
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<pre style="margin: 0;">+<span id="LC1387" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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1388
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<pre style="margin: 0;">+<span id="LC1388" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1389" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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1390
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<pre style="margin: 0;">+<span id="LC1390" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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1391
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<pre style="margin: 0;">+<span id="LC1391" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">s60</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_neon_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">lastTotal</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="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">60</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="mi" style="color: #099;">61</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">61</span><span class="p">];</span></span>
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1392
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<pre style="margin: 0;">+<span id="LC1392" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</span><span class="p">[</span><span class="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">s60</span><span class="p">;</span></span>
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1393
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<pre style="margin: 0;">+<span id="LC1393" class="line" lang="cpp"></span>
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1394
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<pre style="margin: 0;">+<span id="LC1394" class="line" lang="cpp"> <span class="n" style="color: #333;">tT</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">62</span><span class="p">;</span></span>
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1395
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<pre style="margin: 0;">+<span id="LC1395" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">lastTotal2</span><span class="p">;</span></span>
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1396
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<pre style="margin: 0;">+<span id="LC1396" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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1397
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<pre style="margin: 0;">+<span id="LC1397" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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1398
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<pre style="margin: 0;">+<span id="LC1398" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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1399
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<pre style="margin: 0;">+<span id="LC1399" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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1400
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<pre style="margin: 0;">+<span id="LC1400" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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1401
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<pre style="margin: 0;">+<span id="LC1401" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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1402
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<pre style="margin: 0;">+<span id="LC1402" class="line" lang="cpp"></span>
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1403
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<pre style="margin: 0;">+<span id="LC1403" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">s61</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_neon_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">lastTotal2</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="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">60</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="mi" style="color: #099;">61</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">61</span><span class="p">];</span></span>
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1404
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<pre style="margin: 0;">+<span id="LC1404" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</span><span class="p">[</span><span class="mi" style="color: #099;">61</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">s61</span><span class="p">;</span></span>
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1405
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<pre style="margin: 0;">+<span id="LC1405" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC1406" 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;">_neon_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">grandTotal</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s60</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s61</span><span class="p">;</span></span>
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1209
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1407
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<pre style="margin: 0;"> <span id="LC1407" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1408
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<pre style="margin: 0;"> <span id="LC1408" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_product_sum_loop</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62L</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">sum</span><span class="p">);</span></span>
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1211
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1409
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<pre style="margin: 0;"> <span id="LC1409" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1216,7 +1414,7 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList</td>
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1216
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1414
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<pre style="margin: 0;"> <span id="LC1414" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_loop_epilogue</span></span>
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1217
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1415
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<pre style="margin: 0;"> <span id="LC1415" class="line" lang="cpp"> <span class="p">}</span></span>
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1218
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1416
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<pre style="margin: 0;"> <span id="LC1416" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alphabetDimension</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">63UL</span><span class="p">)</span> <span class="p">{</span></span>
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1219
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<pre style="margin: 0;">-<span id="LC1219" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS</span></span>
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<pre style="margin: 0;">+<span id="LC1417" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS<span class="idiff left right"> || defined _SLKP_USE_ARM_NEON</span></span></span>
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1220
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<pre style="margin: 0;"> <span id="LC1418" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_matrix_transpose</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrixT</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1419" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC1420" 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;">siteID</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;">siteID</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;">siteID</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">63L</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1305,6 +1503,51 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList</td>
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1305
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<pre style="margin: 0;"> <span id="LC1503" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</span><span class="p">[</span><span class="mi" style="color: #099;">62</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">s62</span><span class="p">;</span></span>
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1504
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<pre style="margin: 0;"> <span id="LC1504" class="line" lang="cpp"></span>
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1307
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1505
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<pre style="margin: 0;"> <span id="LC1505" 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;">_sse_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">grandTotal</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s60</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s61</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s62</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1506" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#elif defined _SLKP_USE_ARM_NEON</span></span>
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<pre style="margin: 0;">+<span id="LC1507" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">grandTotal</span></span>
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1508
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<pre style="margin: 0;">+<span id="LC1508" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">nil</span><span class="p">);</span></span>
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1509
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<pre style="margin: 0;">+<span id="LC1509" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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1510
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<pre style="margin: 0;">+<span id="LC1510" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1511
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<pre style="margin: 0;">+<span id="LC1511" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1512
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<pre style="margin: 0;">+<span id="LC1512" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1513
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<pre style="margin: 0;">+<span id="LC1513" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1514
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<pre style="margin: 0;">+<span id="LC1514" class="line" lang="cpp"></span>
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1515
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<pre style="margin: 0;">+<span id="LC1515" class="line" lang="cpp"> <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;">tT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tMatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">63</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">60</span><span class="p">;</span></span>
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1516
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<pre style="margin: 0;">+<span id="LC1516" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">lastTotal</span><span class="p">;</span></span>
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1517
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<pre style="margin: 0;">+<span id="LC1517" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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1518
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<pre style="margin: 0;">+<span id="LC1518" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1519
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<pre style="margin: 0;">+<span id="LC1519" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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1520
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<pre style="margin: 0;">+<span id="LC1520" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1521
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<pre style="margin: 0;">+<span id="LC1521" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1522
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<pre style="margin: 0;">+<span id="LC1522" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1523
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<pre style="margin: 0;">+<span id="LC1523" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">s60</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_neon_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">lastTotal</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="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">60</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="mi" style="color: #099;">61</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">61</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="mi" style="color: #099;">62</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">62</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1524
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<pre style="margin: 0;">+<span id="LC1524" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</span><span class="p">[</span><span class="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">s60</span><span class="p">;</span></span>
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1525
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<pre style="margin: 0;">+<span id="LC1525" class="line" lang="cpp"></span>
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1526
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<pre style="margin: 0;">+<span id="LC1526" class="line" lang="cpp"> <span class="n" style="color: #333;">tT</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">63</span><span class="p">;</span></span>
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1527
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<pre style="margin: 0;">+<span id="LC1527" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">lastTotal2</span><span class="p">;</span></span>
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1528
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<pre style="margin: 0;">+<span id="LC1528" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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1529
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<pre style="margin: 0;">+<span id="LC1529" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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1530
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<pre style="margin: 0;">+<span id="LC1530" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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1531
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<pre style="margin: 0;">+<span id="LC1531" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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1532
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<pre style="margin: 0;">+<span id="LC1532" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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1533
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<pre style="margin: 0;">+<span id="LC1533" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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1534
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<pre style="margin: 0;">+<span id="LC1534" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1535
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<pre style="margin: 0;">+<span id="LC1535" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">s61</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_neon_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">lastTotal2</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="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">60</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="mi" style="color: #099;">61</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">61</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="mi" style="color: #099;">62</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">62</span><span class="p">];;</span></span>
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1536
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<pre style="margin: 0;">+<span id="LC1536" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</span><span class="p">[</span><span class="mi" style="color: #099;">61</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">s61</span><span class="p">;</span></span>
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1537
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<pre style="margin: 0;">+<span id="LC1537" class="line" lang="cpp"></span>
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1538
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<pre style="margin: 0;">+<span id="LC1538" class="line" lang="cpp"> <span class="n" style="color: #333;">tT</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">63</span><span class="p">;</span></span>
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1539
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<pre style="margin: 0;">+<span id="LC1539" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">lastTotal3</span><span class="p">;</span></span>
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1540
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<pre style="margin: 0;">+<span id="LC1540" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal3</span><span class="p">);</span></span>
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1541
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<pre style="margin: 0;">+<span id="LC1541" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal3</span><span class="p">);</span></span>
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1542
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<pre style="margin: 0;">+<span id="LC1542" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal3</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1543" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal3</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1544" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal3</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1545" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal3</span><span class="p">);</span></span>
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1546
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<pre style="margin: 0;">+<span id="LC1546" class="line" lang="cpp"></span>
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1547
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<pre style="margin: 0;">+<span id="LC1547" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">s62</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_neon_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">lastTotal3</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="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">60</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="mi" style="color: #099;">61</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">61</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="mi" style="color: #099;">62</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">62</span><span class="p">];;</span></span>
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1548
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<pre style="margin: 0;">+<span id="LC1548" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</span><span class="p">[</span><span class="mi" style="color: #099;">62</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">s62</span><span class="p">;</span></span>
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1549
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<pre style="margin: 0;">+<span id="LC1549" class="line" lang="cpp"></span>
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1550
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<pre style="margin: 0;">+<span id="LC1550" 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;">_neon_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">grandTotal</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s60</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s61</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s62</span><span class="p">;</span></span>
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1308
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1551
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<pre style="margin: 0;"> <span id="LC1551" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1309
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1552
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<pre style="margin: 0;"> <span id="LC1552" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_product_sum_loop</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63L</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">sum</span><span class="p">);</span></span>
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1310
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1553
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<pre style="margin: 0;"> <span id="LC1553" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1568" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1568,7 +1811,7 @@ void _TheTree::ComputeBranchCache (</td>
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1811
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<pre style="margin: 0;"> <span id="LC1811" class="line" lang="cpp"> <span class="n" style="color: #333;">myParent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flatParents</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">myParent</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">flatLeaves</span><span class="p">.</span><span class="n" style="color: #333;">lLength</span><span class="p">];</span></span>
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1812
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<pre style="margin: 0;"> <span id="LC1812" 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;">myParent</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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1570
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1813
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<pre style="margin: 0;"> <span id="LC1813" class="line" lang="cpp"></span>
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1571
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<pre style="margin: 0;">-<span id="LC1571" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS</span></span>
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1814
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<pre style="margin: 0;">+<span id="LC1814" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS<span class="idiff left right"> || defined _SLKP_USE_ARM_NEON</span></span></span>
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1572
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<td class="diff-line-num new_line" data-linenumber="1815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1815
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<pre style="margin: 0;"> <span id="LC1815" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tMatrixT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nil</span><span class="p">;</span></span>
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1573
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1816
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<pre style="margin: 0;"> <span id="LC1816" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">alphabetDimension</span><span class="p">)</span> <span class="p">{</span></span>
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1574
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1817
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<pre style="margin: 0;"> <span id="LC1817" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">20</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">@@ -1755,11 +1998,20 @@ void _TheTree::ComputeBranchCache (</td>
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1755
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1998
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<pre style="margin: 0;"> <span id="LC1998" class="line" lang="cpp"> </span>
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1756
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1999
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<pre style="margin: 0;"> <span id="LC1999" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alphabetDimension</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4L</span><span class="p">)</span> <span class="p">{</span></span>
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1757
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2000
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<pre style="margin: 0;"> <span id="LC2000" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_AVX_INTRINSICS</span></span>
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1758
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<pre style="margin: 0;">-<span id="LC1758" class="line" lang="cpp"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">tmatrix_transpose</span> <span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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1759
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<pre style="margin: 0;">-<span id="LC1759" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">__m256d</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">12</span><span class="p">]},</span></span>
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1760
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<pre style="margin: 0;">-<span id="LC1760" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">__m256d</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">13</span><span class="p">]},</span></span>
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1761
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<pre style="margin: 0;">-<span id="LC1761" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">__m256d</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">14</span><span class="p">]},</span></span>
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1762
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<pre style="margin: 0;">-<span id="LC1762" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">__m256d</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">15</span><span class="p">]}</span></span>
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2001
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<pre style="margin: 0;">+<span id="LC2001" class="line" lang="cpp"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">tmatrix_transpose</span> <span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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2002
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<pre style="margin: 0;">+<span id="LC2002" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">__m256d</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">12</span><span class="p">]},</span></span>
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2003
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<pre style="margin: 0;">+<span id="LC2003" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">__m256d</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">13</span><span class="p">]},</span></span>
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2004
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<pre style="margin: 0;">+<span id="LC2004" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">__m256d</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">14</span><span class="p">]},</span></span>
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2005
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<pre style="margin: 0;">+<span id="LC2005" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">__m256d</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">15</span><span class="p">]}</span></span>
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2006
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<pre style="margin: 0;">+<span id="LC2006" class="line" lang="cpp"> <span class="p">};</span></span>
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2007
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<pre style="margin: 0;">+<span id="LC2007" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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2008
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<pre style="margin: 0;">+<span id="LC2008" class="line" lang="cpp"></span>
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2009
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<pre style="margin: 0;">+<span id="LC2009" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_ARM_NEON</span></span>
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2010
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<pre style="margin: 0;">+<span id="LC2010" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2x2_t</span> <span class="n" style="color: #333;">tmatrix_transpose</span> <span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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2011
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<pre style="margin: 0;">+<span id="LC2011" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">float64x2x2_t</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">12</span><span class="p">]},</span></span>
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2012
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<pre style="margin: 0;">+<span id="LC2012" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">float64x2x2_t</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">13</span><span class="p">]},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2013
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<pre style="margin: 0;">+<span id="LC2013" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">float64x2x2_t</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">14</span><span class="p">]},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2014
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<pre style="margin: 0;">+<span id="LC2014" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">float64x2x2_t</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">],</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="mi" style="color: #099;">15</span><span class="p">]}</span></span>
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1763
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<td class="diff-line-num new_line" data-linenumber="2015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2015
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<pre style="margin: 0;"> <span id="LC2015" class="line" lang="cpp"> <span class="p">};</span></span>
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1764
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<td class="diff-line-num new_line" data-linenumber="2016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2016
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<pre style="margin: 0;"> <span id="LC2016" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1765
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2017
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<pre style="margin: 0;"> <span id="LC2017" 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;">siteID</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;">siteID</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;">siteID</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">4L</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1773" style="width: 35px; color: rgba(0,0,0,0.3); 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="2025" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1773,7 +2025,7 @@ void _TheTree::ComputeBranchCache (</td>
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1773
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2025
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<pre style="margin: 0;"> <span id="LC2025" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1774
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2026
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<pre style="margin: 0;"> <span id="LC2026" class="line" lang="cpp"> <span class="p">}</span></span>
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1775
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2027
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<pre style="margin: 0;"> <span id="LC2027" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">didScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1776
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<td class="diff-line-num new_line old" data-linenumber="2028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1776" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if<span class="idiff left right">def _SLKP_USE_AVX_INTRINSICS</span></span></span>
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2028
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<pre style="margin: 0;">+<span id="LC2028" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if<span class="idiff left right"> defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_ARM_NEON</span></span></span>
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1777
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<td class="diff-line-num new_line" data-linenumber="2029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2029
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<pre style="margin: 0;"> <span id="LC2029" class="line" lang="cpp"> <span class="n" style="color: #333;">_handle4x4_pruning_case</span> <span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">tmatrix_transpose</span><span class="p">);</span></span>
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1778
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<td class="diff-line-num new_line" data-linenumber="2030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2030
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<pre style="margin: 0;"> <span id="LC2030" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1779
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2031
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<pre style="margin: 0;"> <span id="LC2031" class="line" lang="cpp"> <span class="n" style="color: #333;">_handle4x4_pruning_case</span> <span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">nil</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1791" style="width: 35px; color: rgba(0,0,0,0.3); 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="2043" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1791,7 +2043,7 @@ void _TheTree::ComputeBranchCache (</td>
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1791
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2043
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<pre style="margin: 0;"> <span id="LC2043" class="line" lang="cpp"> <span class="n" style="color: #333;">__handle_site_corrections</span><span class="p">(</span><span class="n" style="color: #333;">didScale</span><span class="p">,</span> <span class="n" style="color: #333;">siteID</span><span class="p">);</span></span>
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1792
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2044
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<pre style="margin: 0;"> <span id="LC2044" class="line" lang="cpp"> <span class="p">}</span></span>
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1793
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2045
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<pre style="margin: 0;"> <span id="LC2045" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alphabetDimension</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">20L</span><span class="p">)</span> <span class="p">{</span></span>
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1794
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<pre style="margin: 0;">-<span id="LC1794" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS</span></span>
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2046
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<pre style="margin: 0;">+<span id="LC2046" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS<span class="idiff left right"> || _SLKP_USE_ARM_NEON</span></span></span>
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1795
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2047
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<pre style="margin: 0;"> <span id="LC2047" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_matrix_transpose</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrixT</span><span class="p">);</span></span>
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1796
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2048
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<pre style="margin: 0;"> <span id="LC2048" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1797
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2049
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<pre style="margin: 0;"> <span id="LC2049" 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;">siteID</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;">siteID</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;">siteID</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">20L</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1809" style="width: 35px; color: rgba(0,0,0,0.3); 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="2061" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1809,6 +2061,11 @@ void _TheTree::ComputeBranchCache (</td>
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1809
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2061
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<pre style="margin: 0;"> <span id="LC2061" class="line" lang="cpp"> <span class="n" style="color: #333;">__m128d</span> <span class="n" style="color: #333;">s128</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1810
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2062
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<pre style="margin: 0;"> <span id="LC2062" class="line" lang="cpp"> <span class="n" style="color: #333;">s128</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">20</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">nil</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1811
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<td class="diff-line-num new_line" data-linenumber="2063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2063
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<pre style="margin: 0;"> <span id="LC2063" class="line" lang="cpp"> <span class="n" style="color: #333;">s128</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">20</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">s128</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2064
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<pre style="margin: 0;">+<span id="LC2064" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#elif defined _SLKP_USE_ARM_NEON</span></span>
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2065
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<pre style="margin: 0;">+<span id="LC2065" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdupq_n_f64</span><span class="p">(</span><span class="mf" style="color: #099;">0.</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2066
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<pre style="margin: 0;">+<span id="LC2066" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">20</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">nil</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2067
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<pre style="margin: 0;">+<span id="LC2067" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">20</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">),</span><span class="n" style="color: #333;">grandTotal</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2068
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<pre style="margin: 0;">+<span id="LC2068" 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;">_neon_sum_2</span> <span class="p">(</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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1812
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<td class="diff-line-num new_line" data-linenumber="2069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2069
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<pre style="margin: 0;"> <span id="LC2069" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1813
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2070
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<pre style="margin: 0;"> <span id="LC2070" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_product_sum_loop</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">20L</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">sum</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1814
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2071
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<pre style="margin: 0;"> <span id="LC2071" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1824" style="width: 35px; color: rgba(0,0,0,0.3); 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="2081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1824,7 +2081,7 @@ void _TheTree::ComputeBranchCache (</td>
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1824
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2081
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<pre style="margin: 0;"> <span id="LC2081" class="line" lang="cpp"> <span class="n" style="color: #333;">__handle_site_corrections</span><span class="p">(</span><span class="n" style="color: #333;">didScale</span><span class="p">,</span> <span class="n" style="color: #333;">siteID</span><span class="p">);</span></span>
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1825
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2082
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<pre style="margin: 0;"> <span id="LC2082" class="line" lang="cpp"> <span class="p">}</span></span>
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1826
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2083
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<pre style="margin: 0;"> <span id="LC2083" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alphabetDimension</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">60L</span><span class="p">)</span> <span class="p">{</span></span>
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1827
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<td class="diff-line-num new_line old" data-linenumber="2084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1827" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS</span></span>
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2084
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<pre style="margin: 0;">+<span id="LC2084" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS<span class="idiff left right"> || _SLKP_USE_ARM_NEON</span></span></span>
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1828
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2085
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<pre style="margin: 0;"> <span id="LC2085" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_matrix_transpose</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60L</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrixT</span><span class="p">);</span></span>
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1829
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2086
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<pre style="margin: 0;"> <span id="LC2086" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1830
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2087
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<pre style="margin: 0;"> <span id="LC2087" 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;">siteID</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;">siteID</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;">siteID</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">60L</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1849" style="width: 35px; color: rgba(0,0,0,0.3); 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="2106" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1849,6 +2106,14 @@ void _TheTree::ComputeBranchCache (</td>
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1849
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2106
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<pre style="margin: 0;"> <span id="LC2106" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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1850
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2107
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<pre style="margin: 0;"> <span id="LC2107" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1851
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<td class="diff-line-num new_line" data-linenumber="2108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2108
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<pre style="margin: 0;"> <span id="LC2108" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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2109
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<pre style="margin: 0;">+<span id="LC2109" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#elif defined _SLKP_USE_ARM_NEON</span></span>
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2110
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<pre style="margin: 0;">+<span id="LC2110" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span></span>
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2111
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<pre style="margin: 0;">+<span id="LC2111" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">nil</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2112
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<pre style="margin: 0;">+<span id="LC2112" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2113
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<pre style="margin: 0;">+<span id="LC2113" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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2114
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<pre style="margin: 0;">+<span id="LC2114" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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2115
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<pre style="margin: 0;">+<span id="LC2115" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2116
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<pre style="margin: 0;">+<span id="LC2116" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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1852
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<td class="diff-line-num new_line" data-linenumber="2117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2117
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<pre style="margin: 0;"> <span id="LC2117" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1853
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2118
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<pre style="margin: 0;"> <span id="LC2118" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_product_sum_loop</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60L</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">sum</span><span class="p">);</span></span>
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1854
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2119
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<pre style="margin: 0;"> <span id="LC2119" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2129" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1864,7 +2129,7 @@ void _TheTree::ComputeBranchCache (</td>
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1864
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2129
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<pre style="margin: 0;"> <span id="LC2129" class="line" lang="cpp"> <span class="n" style="color: #333;">__handle_site_corrections</span><span class="p">(</span><span class="n" style="color: #333;">didScale</span><span class="p">,</span> <span class="n" style="color: #333;">siteID</span><span class="p">);</span></span>
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1865
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2130
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<pre style="margin: 0;"> <span id="LC2130" class="line" lang="cpp"> <span class="p">}</span></span>
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1866
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2131
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<pre style="margin: 0;"> <span id="LC2131" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alphabetDimension</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">61L</span><span class="p">)</span> <span class="p">{</span></span>
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1867
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<pre style="margin: 0;">-<span id="LC1867" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS</span></span>
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2132
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<pre style="margin: 0;">+<span id="LC2132" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS<span class="idiff left right"> || defined _SLKP_USE_ARM_NEON</span></span></span>
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1868
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2133
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<pre style="margin: 0;"> <span id="LC2133" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_matrix_transpose</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61L</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrixT</span><span class="p">);</span></span>
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1869
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2134
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<pre style="margin: 0;"> <span id="LC2134" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1870
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2135
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<pre style="margin: 0;"> <span id="LC2135" 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;">siteID</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;">siteID</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;">siteID</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">61L</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1909" style="width: 35px; color: rgba(0,0,0,0.3); 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="2174" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1909,6 +2174,25 @@ void _TheTree::ComputeBranchCache (</td>
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1909
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2174
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<pre style="margin: 0;"> <span id="LC2174" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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1910
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2175
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<pre style="margin: 0;"> <span id="LC2175" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">s60</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_sse_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">lastTotal</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="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">60</span><span class="p">];</span></span>
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1911
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2176
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<pre style="margin: 0;"> <span id="LC2176" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</span><span class="p">[</span><span class="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">s60</span><span class="p">;</span></span>
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2177
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<pre style="margin: 0;">+<span id="LC2177" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#elif defined _SLKP_USE_ARM_NEON</span></span>
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2178
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<pre style="margin: 0;">+<span id="LC2178" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">grandTotal</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2179
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<pre style="margin: 0;">+<span id="LC2179" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">nil</span><span class="p">);</span></span>
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2180
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<pre style="margin: 0;">+<span id="LC2180" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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2181
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<pre style="margin: 0;">+<span id="LC2181" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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2182
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<pre style="margin: 0;">+<span id="LC2182" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2183
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<pre style="margin: 0;">+<span id="LC2183" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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2184
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<pre style="margin: 0;">+<span id="LC2184" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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2185
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<pre style="margin: 0;">+<span id="LC2185" class="line" lang="cpp"></span>
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2186
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<pre style="margin: 0;">+<span id="LC2186" class="line" lang="cpp"> <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;">tT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tMatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">61</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">60</span><span class="p">;</span></span>
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2187
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<pre style="margin: 0;">+<span id="LC2187" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">lastTotal</span><span class="p">;</span></span>
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2188
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<pre style="margin: 0;">+<span id="LC2188" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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2189
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<pre style="margin: 0;">+<span id="LC2189" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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2190
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<pre style="margin: 0;">+<span id="LC2190" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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2191
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<pre style="margin: 0;">+<span id="LC2191" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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2192
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<pre style="margin: 0;">+<span id="LC2192" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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2193
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<pre style="margin: 0;">+<span id="LC2193" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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2194
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<pre style="margin: 0;">+<span id="LC2194" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">s60</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_neon_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">lastTotal</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="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">60</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2195
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<pre style="margin: 0;">+<span id="LC2195" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</span><span class="p">[</span><span class="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">s60</span><span class="p">;</span></span>
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1912
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2196
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<pre style="margin: 0;"> <span id="LC2196" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1913
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2197
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<pre style="margin: 0;"> <span id="LC2197" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_product_sum_loop</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61L</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">sum</span><span class="p">);</span></span>
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1914
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2198
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<pre style="margin: 0;"> <span id="LC2198" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1925" style="width: 35px; color: rgba(0,0,0,0.3); 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="2209" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1925,7 +2209,7 @@ void _TheTree::ComputeBranchCache (</td>
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1925
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2209
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<pre style="margin: 0;"> <span id="LC2209" class="line" lang="cpp"> <span class="n" style="color: #333;">__handle_site_corrections</span><span class="p">(</span><span class="n" style="color: #333;">didScale</span><span class="p">,</span> <span class="n" style="color: #333;">siteID</span><span class="p">);</span></span>
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1926
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2210
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<pre style="margin: 0;"> <span id="LC2210" class="line" lang="cpp"> <span class="p">}</span></span>
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1927
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2211
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<pre style="margin: 0;"> <span id="LC2211" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alphabetDimension</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">62L</span><span class="p">)</span> <span class="p">{</span></span>
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1928
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<pre style="margin: 0;">-<span id="LC1928" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS</span></span>
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2212
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<pre style="margin: 0;">+<span id="LC2212" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS<span class="idiff left right"> || defined _SLKP_USE_ARM_NEON</span></span></span>
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1929
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2213
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<pre style="margin: 0;"> <span id="LC2213" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_matrix_transpose</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62L</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrixT</span><span class="p">);</span></span>
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1930
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2214
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<pre style="margin: 0;"> <span id="LC2214" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1931
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2215
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<pre style="margin: 0;"> <span id="LC2215" 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;">siteID</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;">siteID</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;">siteID</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">62L</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1990" style="width: 35px; color: rgba(0,0,0,0.3); 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="2274" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1990,6 +2274,36 @@ void _TheTree::ComputeBranchCache (</td>
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1990
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2274
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<pre style="margin: 0;"> <span id="LC2274" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1991
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<td class="diff-line-num new_line" data-linenumber="2275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2275
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<pre style="margin: 0;"> <span id="LC2275" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">s61</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_sse_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">lastTotal2</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="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">60</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="mi" style="color: #099;">61</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">61</span><span class="p">];</span></span>
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1992
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2276
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<pre style="margin: 0;"> <span id="LC2276" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</span><span class="p">[</span><span class="mi" style="color: #099;">61</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">s61</span><span class="p">;</span></span>
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2277
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<pre style="margin: 0;">+<span id="LC2277" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#elif defined _SLKP_USE_ARM_NEON</span></span>
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2278
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<pre style="margin: 0;">+<span id="LC2278" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">grandTotal</span></span>
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2279
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<pre style="margin: 0;">+<span id="LC2279" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">nil</span><span class="p">);</span></span>
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2280
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<pre style="margin: 0;">+<span id="LC2280" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2281
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<pre style="margin: 0;">+<span id="LC2281" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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2282
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<pre style="margin: 0;">+<span id="LC2282" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2283
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<pre style="margin: 0;">+<span id="LC2283" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2284
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<pre style="margin: 0;">+<span id="LC2284" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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2285
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<pre style="margin: 0;">+<span id="LC2285" class="line" lang="cpp"></span>
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2286
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<pre style="margin: 0;">+<span id="LC2286" class="line" lang="cpp"> <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;">tT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tMatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">62</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">60</span><span class="p">;</span></span>
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2287
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<pre style="margin: 0;">+<span id="LC2287" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">lastTotal</span><span class="p">;</span></span>
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2288
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<pre style="margin: 0;">+<span id="LC2288" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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2289
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<pre style="margin: 0;">+<span id="LC2289" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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2290
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<pre style="margin: 0;">+<span id="LC2290" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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2291
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<pre style="margin: 0;">+<span id="LC2291" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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2292
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<pre style="margin: 0;">+<span id="LC2292" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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2293
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<pre style="margin: 0;">+<span id="LC2293" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2294
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<pre style="margin: 0;">+<span id="LC2294" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">s60</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_neon_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">lastTotal</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="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">60</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="mi" style="color: #099;">61</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">61</span><span class="p">];</span></span>
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2295
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<pre style="margin: 0;">+<span id="LC2295" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</span><span class="p">[</span><span class="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">s60</span><span class="p">;</span></span>
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2296
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<pre style="margin: 0;">+<span id="LC2296" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="2297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2297
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<pre style="margin: 0;">+<span id="LC2297" class="line" lang="cpp"> <span class="n" style="color: #333;">tT</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">62</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2298
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<pre style="margin: 0;">+<span id="LC2298" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">lastTotal2</span><span class="p">;</span></span>
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2299
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<pre style="margin: 0;">+<span id="LC2299" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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2300
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<pre style="margin: 0;">+<span id="LC2300" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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2301
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<pre style="margin: 0;">+<span id="LC2301" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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2302
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<pre style="margin: 0;">+<span id="LC2302" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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2303
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<pre style="margin: 0;">+<span id="LC2303" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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2304
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<pre style="margin: 0;">+<span id="LC2304" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2305
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<pre style="margin: 0;">+<span id="LC2305" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">s61</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_neon_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">lastTotal2</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="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">60</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="mi" style="color: #099;">61</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">61</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2306
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<pre style="margin: 0;">+<span id="LC2306" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</span><span class="p">[</span><span class="mi" style="color: #099;">61</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">s61</span><span class="p">;</span></span>
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1993
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<td class="diff-line-num new_line" data-linenumber="2307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2307
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<pre style="margin: 0;"> <span id="LC2307" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1994
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<td class="diff-line-num new_line" data-linenumber="2308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2308
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<pre style="margin: 0;"> <span id="LC2308" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_product_sum_loop</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62L</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">sum</span><span class="p">);</span></span>
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1995
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<td class="diff-line-num new_line" data-linenumber="2309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2309
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<pre style="margin: 0;"> <span id="LC2309" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2005" style="width: 35px; color: rgba(0,0,0,0.3); 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="2319" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2005,7 +2319,7 @@ void _TheTree::ComputeBranchCache (</td>
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2005
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<td class="diff-line-num new_line" data-linenumber="2319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2319
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<pre style="margin: 0;"> <span id="LC2319" class="line" lang="cpp"> <span class="n" style="color: #333;">__handle_site_corrections</span><span class="p">(</span><span class="n" style="color: #333;">didScale</span><span class="p">,</span> <span class="n" style="color: #333;">siteID</span><span class="p">);</span></span>
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2006
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<td class="diff-line-num new_line" data-linenumber="2320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2320
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<pre style="margin: 0;"> <span id="LC2320" class="line" lang="cpp"> <span class="p">}</span></span>
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2007
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<td class="diff-line-num new_line" data-linenumber="2321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2321
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<pre style="margin: 0;"> <span id="LC2321" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alphabetDimension</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">63L</span><span class="p">)</span> <span class="p">{</span></span>
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2008
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<pre style="margin: 0;">-<span id="LC2008" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS</span></span>
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2322
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<pre style="margin: 0;">+<span id="LC2322" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS || defined _SLKP_USE_SSE_INTRINSICS<span class="idiff left right"> || defined _SLKP_USE_ARM_NEON</span></span></span>
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2009
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2323
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<pre style="margin: 0;"> <span id="LC2323" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_matrix_transpose</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63L</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrixT</span><span class="p">);</span></span>
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2010
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2324
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<pre style="margin: 0;"> <span id="LC2324" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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2011
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2325
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<pre style="margin: 0;"> <span id="LC2325" 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;">siteID</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;">siteID</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;">siteID</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">63L</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2089" style="width: 35px; color: rgba(0,0,0,0.3); 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="2403" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2089,6 +2403,48 @@ void _TheTree::ComputeBranchCache (</td>
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2089
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2403
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<pre style="margin: 0;"> <span id="LC2403" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal3</span><span class="p">);</span></span>
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2090
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2404
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<pre style="margin: 0;"> <span id="LC2404" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">s62</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_sse_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">lastTotal3</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="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">60</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="mi" style="color: #099;">61</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">61</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="mi" style="color: #099;">62</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">62</span><span class="p">];</span></span>
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2091
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2405
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<pre style="margin: 0;"> <span id="LC2405" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</span><span class="p">[</span><span class="mi" style="color: #099;">62</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">s62</span><span class="p">;</span></span>
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2406
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<pre style="margin: 0;">+<span id="LC2406" class="line" lang="cpp"> </span>
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2407
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<pre style="margin: 0;">+<span id="LC2407" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#elif defined _SLKP_USE_ARM_NEON</span></span>
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2408
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<pre style="margin: 0;">+<span id="LC2408" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span></span>
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2409
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<pre style="margin: 0;">+<span id="LC2409" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">nil</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2410
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<pre style="margin: 0;">+<span id="LC2410" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2411
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<pre style="margin: 0;">+<span id="LC2411" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2412
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<pre style="margin: 0;">+<span id="LC2412" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2413
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<pre style="margin: 0;">+<span id="LC2413" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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2414
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<pre style="margin: 0;">+<span id="LC2414" class="line" lang="cpp"> <span class="n" style="color: #333;">grandTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__ll_handle_block10_product_sum</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrixT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">grandTotal</span><span class="p">);</span></span>
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2415
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<pre style="margin: 0;">+<span id="LC2415" class="line" lang="cpp"></span>
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2416
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<pre style="margin: 0;">+<span id="LC2416" class="line" lang="cpp"> <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;">tT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tMatrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">63</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">60</span><span class="p">;</span></span>
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2417
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<pre style="margin: 0;">+<span id="LC2417" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">lastTotal</span><span class="p">;</span></span>
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2418
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<pre style="margin: 0;">+<span id="LC2418" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2419
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<pre style="margin: 0;">+<span id="LC2419" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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2420
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<pre style="margin: 0;">+<span id="LC2420" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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2421
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<pre style="margin: 0;">+<span id="LC2421" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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2422
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<pre style="margin: 0;">+<span id="LC2422" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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2423
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<pre style="margin: 0;">+<span id="LC2423" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2424
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<pre style="margin: 0;">+<span id="LC2424" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">s60</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_neon_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">lastTotal</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="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">60</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="mi" style="color: #099;">61</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">61</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="mi" style="color: #099;">62</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">62</span><span class="p">];</span></span>
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2425
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<pre style="margin: 0;">+<span id="LC2425" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</span><span class="p">[</span><span class="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">s60</span><span class="p">;</span></span>
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2426
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<pre style="margin: 0;">+<span id="LC2426" class="line" lang="cpp"></span>
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2427
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<pre style="margin: 0;">+<span id="LC2427" class="line" lang="cpp"> <span class="n" style="color: #333;">tT</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">63</span><span class="p">;</span></span>
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2428
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<pre style="margin: 0;">+<span id="LC2428" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">lastTotal2</span><span class="p">;</span></span>
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2429
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<pre style="margin: 0;">+<span id="LC2429" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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2430
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<pre style="margin: 0;">+<span id="LC2430" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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2431
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<pre style="margin: 0;">+<span id="LC2431" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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2432
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<pre style="margin: 0;">+<span id="LC2432" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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2433
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<pre style="margin: 0;">+<span id="LC2433" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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2434
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<pre style="margin: 0;">+<span id="LC2434" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal2</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2435
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<pre style="margin: 0;">+<span id="LC2435" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">s61</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_neon_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">lastTotal2</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="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">60</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="mi" style="color: #099;">61</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">61</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="mi" style="color: #099;">62</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">62</span><span class="p">];</span></span>
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2436
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<pre style="margin: 0;">+<span id="LC2436" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</span><span class="p">[</span><span class="mi" style="color: #099;">61</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">s61</span><span class="p">;</span></span>
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2437
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<pre style="margin: 0;">+<span id="LC2437" class="line" lang="cpp"></span>
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2438
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<pre style="margin: 0;">+<span id="LC2438" class="line" lang="cpp"> <span class="n" style="color: #333;">tT</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">63</span><span class="p">;</span></span>
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2439
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<pre style="margin: 0;">+<span id="LC2439" class="line" lang="cpp"> <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">lastTotal3</span><span class="p">;</span></span>
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2440
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<pre style="margin: 0;">+<span id="LC2440" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal3</span><span class="p">);</span></span>
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2441
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<pre style="margin: 0;">+<span id="LC2441" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal3</span><span class="p">);</span></span>
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2442
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<pre style="margin: 0;">+<span id="LC2442" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal3</span><span class="p">);</span></span>
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2443
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<pre style="margin: 0;">+<span id="LC2443" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal3</span><span class="p">);</span></span>
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2444
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<pre style="margin: 0;">+<span id="LC2444" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal3</span><span class="p">);</span></span>
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2445
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<pre style="margin: 0;">+<span id="LC2445" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_block10_product_sum_linear</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="p">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tT</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lastTotal3</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2446" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">s62</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_neon_sum_2</span><span class="p">(</span><span class="n" style="color: #333;">lastTotal3</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="mi" style="color: #099;">60</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">60</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="mi" style="color: #099;">61</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">61</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="mi" style="color: #099;">62</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tT</span><span class="p">[</span><span class="mi" style="color: #099;">62</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC2447" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</span><span class="p">[</span><span class="mi" style="color: #099;">62</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">s62</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2448" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;"> <span id="LC2449" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_product_sum_loop</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63L</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">sum</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2450" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/e5c8fd32984d059ec09233aa8f7e5cdb888c538c#4ca2d78a3895acfaccf8d26bda9d0ec8aefb2c65"><strong>src/lib/setup.py</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">@@ -5,7 +5,6 @@ from os import path</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">glob</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">glob</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">platform</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">architecture</span><span class="p">,</span> <span class="n" style="color: #333;">mac_ver</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#incdir = get_python_inc(plat_specific=1)</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#print incdir</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">@@ -48,8 +47,10 @@ includePaths += [linkPath, contribPath, sqlitePath]</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"><span class="n" style="color: #333;">define_macros</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="s" style="color: #d14;">'__HYPHY_64__'</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)]</span> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'64'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">architecture</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># openmp on Mac OS X Lion is broken</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"><span class="n" style="color: #333;">major</span><span class="p">,</span> <span class="n" style="color: #333;">minor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mac_ver</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"><span class="n" style="color: #333;">openmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'-fopenmp'</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">major</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">10</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">major</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">10</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">minor</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">7</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#major, minor = mac_ver()[0].split('.')</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#openmp = ['-fopenmp'] if int(major) < 10 or (int(major) == 10 and int(minor) < 7) else []</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"><span class="n" style="color: #333;">openmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'HyPhy'</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">@@ -59,7 +60,7 @@ setup(</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">author_email</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'spond@temple.edu'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'http://www.hyphy.org/'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">packages</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'HyPhy'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">package_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'HyPhy'</span><span class="p">:</span> <span class="s" style="color: #d14;">'<span class="idiff left right">LibraryModules/Python/HyPhy</span>'</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">package_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'HyPhy'</span><span class="p">:</span> <span class="s" style="color: #d14;">'<span class="idiff left right">./</span>'</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># data_files = resFiles,</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># py_modules = ['HyPhy'],</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">ext_modules</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">'_HyPhy'</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">@@ -2,28 +2,28 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">*** RUNNING SINGLE RATE MODEL ***</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">#################################</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">>Done in <span class="idiff left right">5</span> seconds </span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">>Done in <span class="idiff left right">3</span> seconds </span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">-1137.688<span class="idiff left right">42968708</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">-1137.688<span class="idiff left right">70195817</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">-----------------------------------</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">dN/dS = 0.90<span class="idiff left right">51395450601901</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">dN/dS = 0.90<span class="idiff left right">71719918589423</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">*** RUNNING MODEL 1 (Neutral) ***</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">######################################</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">>Done in <span class="idiff left right">3</span> seconds </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">>Done in <span class="idiff left right">2</span> seconds </span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">-1114.6419<span class="idiff left right">7979838</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">-1114.6419<span class="idiff left right">0562717</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">------------------------------------------------</span>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">dN/dS = 0.554<span class="idiff left right">9192972885679 (sample variance = 0.2120268320358276</span>)</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">dN/dS = 0.554<span class="idiff left right">8244466259989 (sample variance = 0.2120544773207587</span>)</span>
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24
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">Rate[1]= 0.078<span class="idiff left right">54090 (weight=0.4830173</span>)</span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">Rate[2]= 1.00000000 (weight=0.5169<span class="idiff left right">827</span>)</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Rate[1]= 0.078<span class="idiff left right">48545 (weight=0.4830912</span>)</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Rate[2]= 1.00000000 (weight=0.5169<span class="idiff left right">088</span>)</span>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">------------------------------------------------</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">@@ -37,215 +37,215 @@ Import the following part into a data processing program</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">for further analysis</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">Rate/Site Rate=0.078<span class="idiff left right">54089951899505</span> Rate=1</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">1 0.00041<span class="idiff left right">54841702208897 0.9995845158297791</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">2 0.949<span class="idiff left right">4800946553694 0.05051990534463052</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">3 0.852<span class="idiff left right">7138076557068 0.1472861923442931</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext">4 0.977<span class="idiff left right">2953209605599 0.02270467903944003</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">5 0.70<span class="idiff left right">89270358876215 0.2910729641123</span>785</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">6 0.9706<span class="idiff left right">034286518881 0.02939657134811178</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">12 0.80<span class="idiff left right">39911310919982 0.196008868908001</span>8</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext">24 7.0<span class="idiff left right">60663427640608e-05 0.9999293933657236</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext">26 2.23<span class="idiff left right">9754017472222e-05 0.9999776024598254</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext">28 1.8<span class="idiff left right">23968038733901e-08 0.999999981760319</span>7</span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext">31 0.00237<span class="idiff left right">9358355164586 0.997620641644835</span>4</span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">37 0.063<span class="idiff left right">36691422415654 0.936633085775843</span>4</span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext">39 0.00191<span class="idiff left right">9852660566921 0.998080147339433</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext">41 0.529<span class="idiff left right">4498773319029 0.470550122668097</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext">42 0.838<span class="idiff left right">3792474897703 0.1616207525102296</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext">43 0.592<span class="idiff left right">1771900482152 0.4078228099517847</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext">44 0.208<span class="idiff left right">194488060306 0.791805511939694</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext">45 0.481<span class="idiff left right">2547391790605 0.5187452608209394</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext">46 0.01854<span class="idiff left right">854305069108 0.9814514569493089</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="plaintext">47 0.76<span class="idiff left right">38290038081602 0.2361709961918397</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext">48 0.140<span class="idiff left right">2805111076657 0.8597194888923344</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext">49 0.076<span class="idiff left right">49019370504373 0.9235098062949563</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext">50 0.55<span class="idiff left right">65553788637815 0.443444621136218</span>5</span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext">51 4.<span class="idiff left right">401412699981744e-06 0.9999955985873</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext">52 0.968<span class="idiff left right">6853075822512 0.03131469241774875</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext">53 0.933<span class="idiff left right">7995342113474 0.0662004657886525</span>3</span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext">54 0.0571<span class="idiff left right">3111117495385 0.9428688888250462</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext">55 0.673<span class="idiff left right">3962368122044 0.3266037631877956</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext">56 0.978<span class="idiff left right">5832556654707 0.02141674433452926</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="plaintext">57 0.0363<span class="idiff left right">8999158091847 0.9636100084190816</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="plaintext">58 0.936<span class="idiff left right">6001361131814 0.0633998638868185</span>2</span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="plaintext">59 0.02363<span class="idiff left right">153610583355 0.9763684638941664</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="plaintext">60 0.71<span class="idiff left right">57862269098134 0.2842137730901866</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="plaintext">61 0.274<span class="idiff left right">0628614189302 0.7259371385810699</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="plaintext">62 0.172<span class="idiff left right">0628516827533 0.8279371483172466</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="plaintext">63 0.06<span class="idiff left right">696027896282203 0.933039721037178</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="plaintext">64 0.159<span class="idiff left right">0255451412893 0.8409744548587106</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="plaintext">65 0.137<span class="idiff left right">1557240403739 0.8628442759596261</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext">66 2.8<span class="idiff left right">3460436728884e-08 0.9999999716539563</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="plaintext">67 0.539<span class="idiff left right">0460493463879 0.4609539506536121</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="plaintext">68 0.000662<span class="idiff left right">8127730370201 0.99933718722696</span>3</span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="plaintext">69 2.8<span class="idiff left right">73441346176776e-05 0.9999712655865381</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="plaintext">70 0.323<span class="idiff left right">4733611365553 0.6765266388634448</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="plaintext">71 0.22<span class="idiff left right">49283193971887 0.7750716806028114</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="plaintext">72 0.16<span class="idiff left right">1927560424059 0.8380724395759409</span></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="plaintext">73 0.1394<span class="idiff left right">764462745381 0.860523553725461</span>9</span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="plaintext">74 0.949<span class="idiff left right">4800946553694 0.05051990534463052</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="plaintext">75 0.02458<span class="idiff left right">202885075857 0.9754179711492413</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="plaintext">76 6.4<span class="idiff left right">11295676480708e-05 0.9999358870432352</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="plaintext">77 0.971<span class="idiff left right">5441430178714 0.02845585698212867</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="plaintext">78 0.786<span class="idiff left right">2785460776877 0.213721453922312</span>4</span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="plaintext">79 0.73<span class="idiff left right">28737186780433 0.2671262813219566</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="plaintext">80 0.9706<span class="idiff left right">034286518881 0.02939657134811178</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="plaintext">81 0.861<span class="idiff left right">1706364190057 0.138829363580994</span>4</span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="plaintext">82 0.76<span class="idiff left right">68224471831266 0.2331775528168733</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="plaintext">83 5.6<span class="idiff left right">72677285259407e-05 0.9999432732271474</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="plaintext">84 0.0067<span class="idiff left right">41759929513022 0.99325824007048</span>7</span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="plaintext">85 0.968<span class="idiff left right">36526712463 0.03163473287536989</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="plaintext">86 0.968<span class="idiff left right">6853075822512 0.03131469241774875</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="plaintext">87 1.5<span class="idiff left right">31106965534881e-05 0.999984688930344</span>6</span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="plaintext">88 0.76<span class="idiff left right">68224471831266 0.2331775528168733</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="plaintext">89 0.931<span class="idiff left right">6117506366601 0.0683882493633398</span>1</span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="plaintext">90 0.0386<span class="idiff left right">175672192274 0.9613824327807726</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="plaintext">91 0.587<span class="idiff left right">2082036930426 0.4127917963069574</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Rate/Site Rate=0.078<span class="idiff left right">48544796897376</span> Rate=1</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">2 0.949<span class="idiff left right">615551955995 0.05038444804400498</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">3 0.852<span class="idiff left right">9359368370378 0.1470640631629622</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">4 0.977<span class="idiff left right">3716102717996 0.02262838972820037</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">5 0.70<span class="idiff left right">91414936372149 0.290858506362</span>785</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">6 0.9706<span class="idiff left right">969154415642 0.02930308455843569</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">7 0.841<span class="idiff left right">382629288338 0.158617370711662</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">8 0.64<span class="idiff left right">50287771422856 0.3549712228577144</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">9 0.0090<span class="idiff left right">17591385717552 0.9909824086142826</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">10 0.251<span class="idiff left right">7327512397574 0.7482672487602428</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">11 0.936<span class="idiff left right">4355050188269 0.06356449498117313</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">12 0.80<span class="idiff left right">42392149007731 0.195760785099226</span>8</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">13 0.959<span class="idiff left right">4019831567395 0.04059801684326048</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">14 0.683<span class="idiff left right">3362390928011 0.316663760907199</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">15 0.968<span class="idiff left right">7756816361081 0.03122431836389203</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">16 0.968<span class="idiff left right">7756816361081 0.03122431836389203</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">17 0.949<span class="idiff left right">615551955995 0.05038444804400498</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">18 0.0962<span class="idiff left right">6486184129626 0.903735138158703</span>7</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">19 0.804<span class="idiff left right">8657022558181 0.1951342977441818</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">20 0.425<span class="idiff left right">8332890773215 0.5741667109226785</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">21 0.001162<span class="idiff left right">544759598141 0.9988374552404018</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">22 0.0011<span class="idiff left right">7934284219372 0.9988206571578063</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">23 0.949<span class="idiff left right">615551955995 0.05038444804400498</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">24 7.0<span class="idiff left right">5692249317919e-05 0.9999294307750682</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">25 0.860<span class="idiff left right">2498450519684 0.1397501549480315</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">26 2.23<span class="idiff left right">5787126908494e-05 0.9999776421287309</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">27 0.71<span class="idiff left right">60075322697251 0.2839924677302748</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">28 1.8<span class="idiff left right">1694382789184e-08 0.999999981830561</span>7</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">29 0.978<span class="idiff left right">655781308275 0.02134421869172495</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">30 0.582<span class="idiff left right">5330972325473 0.4174669027674526</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">31 0.00237<span class="idiff left right">797957064055 0.997622020429359</span>4</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">32 0.841<span class="idiff left right">382629288338 0.158617370711662</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">33 0.936<span class="idiff left right">4355050188269 0.06356449498117313</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">34 0.69<span class="idiff left right">84640898990011 0.3015359101009989</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">35 0.778<span class="idiff left right">8646013536071 0.2211353986463928</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">36 0.0142<span class="idiff left right">2156141350081 0.9857784385864992</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">37 0.063<span class="idiff left right">42743744187564 0.936572562558124</span>4</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">38 0.691<span class="idiff left right">7494525406751 0.3082505474593248</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">39 0.00191<span class="idiff left right">842922725556 0.9980815707727445</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">40 0.00396<span class="idiff left right">2940766435124 0.9960370592335649</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">41 0.529<span class="idiff left right">9471303854615 0.4700528696145386</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">42 0.838<span class="idiff left right">5993998396862 0.1614006001603138</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">43 0.592<span class="idiff left right">3948163573549 0.407605183642645</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">44 0.208<span class="idiff left right">5284079556125 0.7914715920443876</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">45 0.481<span class="idiff left right">6557620682597 0.5183442379317403</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">46 0.01854<span class="idiff left right">486833821928 0.9814551316617807</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">47 0.76<span class="idiff left right">40484766915798 0.2359515233084201</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">48 0.140<span class="idiff left right">4682371700924 0.8595317628299075</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">49 0.076<span class="idiff left right">57491682608442 0.9234250831739156</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">50 0.55<span class="idiff left right">70427216616054 0.442957278338394</span>5</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">51 4.<span class="idiff left right">395262579126055e-06 0.9999956047374209</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">52 0.968<span class="idiff left right">7756816361081 0.03122431836389203</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">53 0.933<span class="idiff left right">9655403783996 0.0660344596216004</span>3</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">54 0.0571<span class="idiff left right">76351410101 0.942823648589899</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">55 0.673<span class="idiff left right">8749864466691 0.3261250135533308</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">56 0.978<span class="idiff left right">655781308275 0.02134421869172495</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">57 0.0363<span class="idiff left right">9242086085162 0.9636075791391484</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">58 0.936<span class="idiff left right">7572417729919 0.0632427582270081</span>2</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">59 0.02363<span class="idiff left right">022019514807 0.9763697798048518</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">60 0.71<span class="idiff left right">60075322697251 0.2839924677302748</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">61 0.274<span class="idiff left right">2154507693895 0.7257845492306105</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">62 0.172<span class="idiff left right">1183776736239 0.8278816223263761</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">63 0.06<span class="idiff left right">701858054585133 0.9329814194541487</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">64 0.159<span class="idiff left right">2881364653803 0.8407118635346197</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">65 0.137<span class="idiff left right">3340643424358 0.8626659356575642</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">66 2.8<span class="idiff left right">27881136893144e-08 0.9999999717211886</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">67 0.539<span class="idiff left right">1574881592042 0.4608425118407958</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">68 0.000662<span class="idiff left right">2339418346806 0.999337766058165</span>3</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">69 2.8<span class="idiff left right">66242595935145e-05 0.9999713375740407</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">70 0.323<span class="idiff left right">7224918056043 0.6762775081943957</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">71 0.22<span class="idiff left right">50277291358384 0.7749722708641616</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">72 0.16<span class="idiff left right">21092944461913 0.8378907055538086</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">73 0.1394<span class="idiff left right">617511496932 0.860538248850306</span>9</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">74 0.949<span class="idiff left right">615551955995 0.05038444804400498</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">75 0.02458<span class="idiff left right">626333717552 0.9754137366628245</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">76 6.4<span class="idiff left right">07045470315398e-05 0.9999359295452969</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">77 0.971<span class="idiff left right">6263288159281 0.02837367118407193</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">78 0.786<span class="idiff left right">4931352062936 0.213506864793706</span>4</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">79 0.73<span class="idiff left right">33948721239267 0.2666051278760733</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">80 0.9706<span class="idiff left right">969154415642 0.02930308455843569</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">81 0.861<span class="idiff left right">3585063476906 0.138641493652309</span>4</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">82 0.76<span class="idiff left right">70412142745399 0.2329587857254601</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">83 5.6<span class="idiff left right">66114976590877e-05 0.9999433388502341</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">84 0.0067<span class="idiff left right">27990372494228 0.993272009627505</span>7</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">85 0.968<span class="idiff left right">4585560287761 0.03154144397122403</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">86 0.968<span class="idiff left right">7756816361081 0.03122431836389203</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">87 1.5<span class="idiff left right">2384846143212e-05 0.999984761515385</span>6</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">88 0.76<span class="idiff left right">70412142745399 0.2329587857254601</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">89 0.931<span class="idiff left right">7501104144779 0.0682498895855221</span>1</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">90 0.0386<span class="idiff left right">2425798799864 0.9613757420120014</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">91 0.587<span class="idiff left right">359366036023 0.4126406339639771</span></span>
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132
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="plaintext"></span>
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133
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="plaintext">*** RUNNING MODEL 2 (Selection) ***</span>
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134
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="plaintext">######################################</span>
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135
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="plaintext"></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="plaintext">>Done in <span class="idiff left right">8</span> seconds </span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">>Done in <span class="idiff left right">6</span> seconds </span>
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137
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="plaintext">-1106.4454<span class="idiff left right">5333916</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">-1106.4454<span class="idiff left right">3364521</span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="plaintext"></span>
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="plaintext">------------------------------------------------</span>
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141
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="plaintext"></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="plaintext">dN/dS = 1.12<span class="idiff left right">9068005488161 (sample variance = 1.588067143267372</span>)</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">dN/dS = 1.12<span class="idiff left right">6641026596627 (sample variance = 1.581382036629081</span>)</span>
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143
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="plaintext"></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="plaintext">Rate[1]= 0.05<span class="idiff left right">854806 (weight=0.3747723</span>)</span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="plaintext">Rate[2]= 1.00000000 (weight=0.44<span class="idiff left right">27396</span>)</span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="plaintext">Rate[3]= 3.64<span class="idiff left right">070986 (weight=0.1824881</span>)</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">Rate[1]= 0.05<span class="idiff left right">768870 (weight=0.3739141</span>)</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">Rate[2]= 1.00000000 (weight=0.44<span class="idiff left right">47790</span>)</span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">Rate[3]= 3.64<span class="idiff left right">184458 (weight=0.1813069</span>)</span>
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="plaintext"></span>
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148
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="plaintext">------------------------------------------------</span>
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149
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="plaintext"></span>
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150
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="plaintext"> Sites with dN/dS>1 (Posterior cutoff = 0.9)</span>
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151
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext"></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="plaintext">26 (0.90<span class="idiff left right">71235888236596</span>)</span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="plaintext">28 (0.999<span class="idiff left right">208561635355</span>)</span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="plaintext">66 (0.9984<span class="idiff left right">823131311625</span>)</span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="plaintext">87 (0.985<span class="idiff left right">639180825136</span>)</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">26 (0.90<span class="idiff left right">5748932682225</span>)</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">28 (0.999<span class="idiff left right">1894014403121</span>)</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">66 (0.9984<span class="idiff left right">584808494847</span>)</span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">87 (0.985<span class="idiff left right">4566318670548</span>)</span>
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="plaintext">------------------------------------------------</span>
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159
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="plaintext"></span>
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160
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="plaintext"> Sites with dN/dS<=1 (Posterior cutoff = 0.9)</span>
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161
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="plaintext"></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="plaintext">1 (0.50<span class="idiff left right">52373923971539</span>)</span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="plaintext">2 (0.00045<span class="idiff left right">93492021371499</span>)</span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="plaintext">3 (0.005<span class="idiff left right">917205452138728</span>)</span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="plaintext">4 (9.<span class="idiff left right">663607149571083</span>e-05)</span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="plaintext">5 (0.031<span class="idiff left right">72842746069128</span>)</span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="plaintext">6 (0.0001<span class="idiff left right">511795330813065</span>)</span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="plaintext">7 (0.006<span class="idiff left right">943635909993886</span>)</span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="plaintext">8 (0.056<span class="idiff left right">73891477006113</span>)</span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="plaintext">9 (0.72<span class="idiff left right">26692280451891</span>)</span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="plaintext">10 (0.09<span class="idiff left right">651028335914213</span>)</span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="plaintext">11 (0.0009<span class="idiff left right">207100403048468</span>)</span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="plaintext">12 (0.010<span class="idiff left right">64028334210353</span>)</span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="plaintext">13 (0.0004<span class="idiff left right">934182636844576</span>)</span>
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="plaintext">14 (0.039<span class="idiff left right">91745163515635</span>)</span>
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="plaintext">15 (0.0002<span class="idiff left right">225580972989534</span>)</span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="plaintext">16 (0.0002<span class="idiff left right">225580972989534</span>)</span>
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="plaintext">17 (0.00045<span class="idiff left right">93492021371499</span>)</span>
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="plaintext">18 (0.43<span class="idiff left right">30406113257519</span>)</span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="plaintext">19 (0.011<span class="idiff left right">6121595707726</span>)</span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="plaintext">20 (0.033<span class="idiff left right">6812685288552</span>)</span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="plaintext">21 (0.24<span class="idiff left right">73118054259542</span>)</span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="plaintext">22 (0.79<span class="idiff left right">84465921549734</span>)</span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="plaintext">23 (0.00045<span class="idiff left right">93492021371499</span>)</span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="plaintext">24 (0.5<span class="idiff left right">842280859182822</span>)</span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="plaintext">25 (0.005<span class="idiff left right">172980464989402</span>)</span>
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="plaintext">27 (0.029<span class="idiff left right">40476216359821</span>)</span>
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="plaintext">29 (7.<span class="idiff left right">95294719517693</span>1e-05)</span>
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="plaintext">30 (0.09<span class="idiff left right">146670281887008</span>)</span>
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="plaintext">31 (0.56<span class="idiff left right">99030448214001</span>)</span>
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="plaintext">32 (0.006<span class="idiff left right">943635909993886</span>)</span>
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="plaintext">33 (0.0009<span class="idiff left right">207100403048468</span>)</span>
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="plaintext">34 (0.004<span class="idiff left right">515364181301996</span>)</span>
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="plaintext">35 (0.0020<span class="idiff left right">50750658840959</span>)</span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="plaintext">36 (0.10<span class="idiff left right">52215418403245</span>)</span>
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="plaintext">37 (0.08<span class="idiff left right">602792425933428</span>)</span>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="plaintext">38 (0.0053<span class="idiff left right">9847934720022</span>6)</span>
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="plaintext">39 (0.64<span class="idiff left right">40044083471241</span>)</span>
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="plaintext">40 (0.45<span class="idiff left right">58311806110331</span>)</span>
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="plaintext">41 (0.011<span class="idiff left right">85264798035508</span>)</span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="plaintext">42 (0.006<span class="idiff left right">857989522987185</span>)</span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="plaintext">43 (0.08<span class="idiff left right">367248274274289</span>)</span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="plaintext">44 (0.011<span class="idiff left right">8366048650329</span>3)</span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="plaintext">45 (0.017<span class="idiff left right">50623812172373</span>)</span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="plaintext">46 (0.42<span class="idiff left right">94127609528174</span>)</span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="plaintext">47 (0.018<span class="idiff left right">3780006215666</span>)</span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="plaintext">48 (0.02<span class="idiff left right">534884977862542</span>)</span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="plaintext">49 (0.0<span class="idiff left right">711274564411852</span>5)</span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="plaintext">50 (0.010<span class="idiff left right">63437293207849</span>)</span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="plaintext">51 (0.88<span class="idiff left right">61014582086777</span>)</span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="plaintext">52 (0.0002<span class="idiff left right">225580972989534</span>)</span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="plaintext">53 (0.0007<span class="idiff left right">683604393760527</span>)</span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="plaintext">54 (0.09<span class="idiff left right">835228649247904</span>)</span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="plaintext">55 (0.006<span class="idiff left right">339545564899368</span>)</span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="plaintext">56 (7.<span class="idiff left right">95294719517693</span>1e-05)</span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="plaintext">57 (0.20<span class="idiff left right">50735349427733</span>)</span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="plaintext">58 (0.0007<span class="idiff left right">27531168723411</span>)</span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="plaintext">59 (0.3<span class="idiff left right">314435529804894</span>)</span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="plaintext">60 (0.029<span class="idiff left right">40476216359821</span>)</span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="plaintext">61 (0.08<span class="idiff left right">200111674080049</span>)</span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="plaintext">62 (0.19<span class="idiff left right">3666026549605</span>)</span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="plaintext">63 (0.07<span class="idiff left right">72513986346591</span>)</span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="plaintext">64 (0.021<span class="idiff left right">48421691961612</span>)</span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="plaintext">65 (0.02<span class="idiff left right">745286636506417</span>)</span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="plaintext">67 (0.12<span class="idiff left right">61823647518457</span>)</span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="plaintext">68 (0.60<span class="idiff left right">5555060135807</span>)</span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="plaintext">69 (0.83<span class="idiff left right">33573458992974</span>)</span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="plaintext">70 (0.05<span class="idiff left right">534546347214257</span>)</span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="plaintext">71 (0.12<span class="idiff left right">27852244756305</span>)</span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="plaintext">72 (0.02<span class="idiff left right">110507208988902</span>)</span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="plaintext">73 (0.27<span class="idiff left right">7601024967129</span>3)</span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="plaintext">74 (0.00045<span class="idiff left right">93492021371499</span>)</span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="plaintext">75 (0.30<span class="idiff left right">73445506286841</span>)</span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="plaintext">76 (0.67<span class="idiff left right">59845714674814</span>)</span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="plaintext">77 (0.0002<span class="idiff left right">305219770671781</span>)</span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="plaintext">78 (0.014<span class="idiff left right">99353952539858</span>)</span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="plaintext">79 (0.003<span class="idiff left right">225300542333516</span>)</span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="plaintext">80 (0.0001<span class="idiff left right">511795330813065</span>)</span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="plaintext">81 (0.005<span class="idiff left right">173815704594973</span>)</span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="plaintext">82 (0.017<span class="idiff left right">77066638393202</span>)</span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="plaintext">83 (0.81<span class="idiff left right">42466349701873</span>)</span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="plaintext">84 (0.27<span class="idiff left right">83391381741632</span>)</span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="plaintext">85 (0.00019<span class="idiff left right">64834081581603</span>)</span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="plaintext">86 (0.0002<span class="idiff left right">225580972989534</span>)</span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="plaintext">88 (0.017<span class="idiff left right">77066638393202</span>)</span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="plaintext">89 (0.0011<span class="idiff left right">73394928906147</span>)</span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="plaintext">90 (0.18<span class="idiff left right">64176575163458</span>)</span>
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248
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="plaintext">91 (0.08<span class="idiff left right">828981163248605</span>)</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">1 (0.50<span class="idiff left right">05649106541394</span>)</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">2 (0.00045<span class="idiff left right">06733110064033</span>)</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">3 (0.005<span class="idiff left right">834191751320087</span>)</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">4 (9.<span class="idiff left right">457380175062416</span>e-05)</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext">5 (0.031<span class="idiff left right">38510059998675</span>)</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">6 (0.0001<span class="idiff left right">480393169770257</span>)</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">7 (0.006<span class="idiff left right">847428124619753</span>)</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext">8 (0.056<span class="idiff left right">19655457626769</span>)</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">9 (0.72<span class="idiff left right">02616116659697</span>)</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">10 (0.09<span class="idiff left right">532197568044432</span>)</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext">11 (0.0009<span class="idiff left right">046734380393297</span>)</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext">12 (0.010<span class="idiff left right">50223976511856</span>)</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">13 (0.0004<span class="idiff left right">847586715730755</span>)</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">14 (0.039<span class="idiff left right">50684521589812</span>)</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext">15 (0.0002<span class="idiff left right">182155996077391</span>)</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext">16 (0.0002<span class="idiff left right">182155996077391</span>)</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext">17 (0.00045<span class="idiff left right">06733110064033</span>)</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">18 (0.43<span class="idiff left right">03827103641656</span>)</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">19 (0.011<span class="idiff left right">46247222682962</span>)</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">20 (0.033<span class="idiff left right">18736449456186</span>)</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">21 (0.24<span class="idiff left right">36354993793777</span>)</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">22 (0.79<span class="idiff left right">62699486165546</span>)</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext">23 (0.00045<span class="idiff left right">06733110064033</span>)</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">24 (0.5<span class="idiff left right">7941118084374</span>)</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">25 (0.005<span class="idiff left right">099728165153801</span>)</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">27 (0.029<span class="idiff left right">08192622556446</span>)</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext">29 (7.<span class="idiff left right">77819701749575</span>1e-05)</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext">30 (0.09<span class="idiff left right">069853965707597</span>)</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">31 (0.56<span class="idiff left right">60401862868557</span>)</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext">32 (0.006<span class="idiff left right">847428124619753</span>)</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">33 (0.0009<span class="idiff left right">046734380393297</span>)</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">34 (0.004<span class="idiff left right">442814164845603</span>)</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">35 (0.0020<span class="idiff left right">16405422878198</span>)</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext">36 (0.10<span class="idiff left right">33806809795843</span>)</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext">37 (0.08<span class="idiff left right">45869735850874</span>)</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext">38 (0.0053<span class="idiff left right">1556911743883</span>6)</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">39 (0.64<span class="idiff left right">04963641339237</span>)</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">40 (0.45<span class="idiff left right">13223091835529</span>)</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext">41 (0.011<span class="idiff left right">66252323108743</span>)</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext">42 (0.006<span class="idiff left right">762560825262604</span>)</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext">43 (0.08<span class="idiff left right">294489462806978</span>)</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext">44 (0.011<span class="idiff left right">5914530997568</span>3)</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext">45 (0.017<span class="idiff left right">23403953949377</span>)</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext">46 (0.42<span class="idiff left right">58799056869767</span>)</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext">47 (0.018<span class="idiff left right">15822194877413</span>)</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext">48 (0.02<span class="idiff left right">48595357138091</span>)</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">49 (0.0<span class="idiff left right">698503880631039</span>5)</span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext">50 (0.010<span class="idiff left right">46813156931801</span>)</span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">51 (0.88<span class="idiff left right">42009233039249</span>)</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext">52 (0.0002<span class="idiff left right">182155996077391</span>)</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext">53 (0.0007<span class="idiff left right">544903027667682</span>)</span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">54 (0.09<span class="idiff left right">676453858925446</span>)</span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext">55 (0.006<span class="idiff left right">243972369370006</span>)</span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext">56 (7.<span class="idiff left right">77819701749575</span>1e-05)</span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext">57 (0.20<span class="idiff left right">24175281590031</span>)</span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext">58 (0.0007<span class="idiff left right">143331590382112</span>)</span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext">59 (0.3<span class="idiff left right">28082302559163</span>)</span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext">60 (0.029<span class="idiff left right">08192622556446</span>)</span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext">61 (0.08<span class="idiff left right">094857058070434</span>)</span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext">62 (0.19<span class="idiff left right">1684602210924</span>)</span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext">63 (0.07<span class="idiff left right">594221099860735</span>)</span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext">64 (0.021<span class="idiff left right">06638033100854</span>)</span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext">65 (0.02<span class="idiff left right">692637587837913</span>)</span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext">67 (0.12<span class="idiff left right">52291578690442</span>)</span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext">68 (0.60<span class="idiff left right">13314754839405</span>)</span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext">69 (0.83<span class="idiff left right">10257634017505</span>)</span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext">70 (0.05<span class="idiff left right">459581602399919</span>)</span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext">71 (0.12<span class="idiff left right">13339421503428</span>)</span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext">72 (0.02<span class="idiff left right">070417777354739</span>)</span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext">73 (0.27<span class="idiff left right">5223067282174</span>3)</span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext">74 (0.00045<span class="idiff left right">06733110064033</span>)</span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext">75 (0.30<span class="idiff left right">40808672019115</span>)</span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext">76 (0.67<span class="idiff left right">16789194025321</span>)</span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext">77 (0.0002<span class="idiff left right">260604432214562</span>)</span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext">78 (0.014<span class="idiff left right">80917575963592</span>)</span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext">79 (0.003<span class="idiff left right">175560377811062</span>)</span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext">80 (0.0001<span class="idiff left right">480393169770257</span>)</span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext">81 (0.005<span class="idiff left right">098851302542715</span>)</span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext">82 (0.017<span class="idiff left right">55686700678069</span>)</span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext">83 (0.81<span class="idiff left right">17048671851982</span>)</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext">84 (0.27<span class="idiff left right">41932110594019</span>)</span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext">85 (0.00019<span class="idiff left right">25217117709219</span>)</span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext">86 (0.0002<span class="idiff left right">182155996077391</span>)</span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext">88 (0.017<span class="idiff left right">55686700678069</span>)</span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext">89 (0.0011<span class="idiff left right">53571766383773</span>)</span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext">90 (0.18<span class="idiff left right">39063827910584</span>)</span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext">91 (0.08<span class="idiff left right">75405164290031</span>)</span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="plaintext"></span>
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250
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="plaintext">------------------------------------------------</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">@@ -256,95 +256,95 @@ Import the following part into a data processing program</td>
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="plaintext">for further analysis</span>
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257
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="plaintext"></span>
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258
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258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="plaintext"></span>
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259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="plaintext">Rate/Site Rate=0.05<span class="idiff left right">854805862606752 Rate=1 Rate=3.640709855148721</span></span>
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260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="plaintext">1 2.<span class="idiff left right">123821587431194e-05 0.4947413693869718 0.5052373923971539</span></span>
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261
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="plaintext">2 0.845<span class="idiff left right">4805150711112 0.1540601357267516 0.0004593492021371499</span></span>
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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="plaintext">3 0.71<span class="idiff left right">71925566791651 0.2768902378686959 0.005917205452138728</span></span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="plaintext">4 0.902<span class="idiff left right">3145803022071 0.09758878362629728 9.663607149571083</span>e-05</span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="plaintext">5 0.58<span class="idiff left right">29266831612094 0.3853448893780992 0.03172842746069128</span></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="plaintext">6 0.887<span class="idiff left right">4735538558555 0.112375266611063 0.0001511795330813065</span></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="plaintext">7 0.70<span class="idiff left right">1299413788691 0.2917569503013152 0.006943635909993886</span></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="plaintext">8 0.52<span class="idiff left right">58486059883327 0.4174124792416061 0.05673891477006113</span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="plaintext">9 0.0010<span class="idiff left right">5308734360597 0.276277684611205 0.7226692280451891</span></span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="plaintext">10 0.<span class="idiff left right">1004481920361048 0.803041524604753 0.09651028335914213</span></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="plaintext">11 0.819<span class="idiff left right">4140603392319 0.1796652296204631 0.0009207100403048468</span></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="plaintext">12 0.67<span class="idiff left right">17772510719154 0.3175824655859811 0.01064028334210353</span></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="plaintext">13 0.864<span class="idiff left right">6165745664404 0.1348900071698753 0.0004934182636844576</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="plaintext">14 0.56<span class="idiff left right">24375756998519 0.3976449726649919 0.03991745163515635</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="plaintext">15 0.882<span class="idiff left right">2191864215847 0.1175582554811163 0.0002225580972989534</span></span>
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="plaintext">16 0.882<span class="idiff left right">2191864215847 0.1175582554811163 0.0002225580972989534</span></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="plaintext">17 0.845<span class="idiff left right">4805150711112 0.1540601357267516 0.0004593492021371499</span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="plaintext">18 0.032<span class="idiff left right">983308732931 0.533976079941317 0.4330406113257519</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="plaintext">19 0.66<span class="idiff left right">45919677056602 0.3237958727235673 0.0116121595707726</span></span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="plaintext">20 0.15<span class="idiff left right">97162578236267 0.806602473647518 0.0336812685288552</span></span>
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="plaintext">21 6.<span class="idiff left right">497561809983018e-05 0.752623218955946 0.2473118054259542</span></span>
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="plaintext">22 <span class="idiff left right">6.147883799728457e-05 0.2014919290070293 0.7984465921549734</span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="plaintext">23 0.845<span class="idiff left right">4805150711112 0.1540601357267516 0.0004593492021371499</span></span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="plaintext">24 1.<span class="idiff left right">810178742010458e-06 0.4157701039029758 0.5842280859182822</span></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="plaintext">25 0.725<span class="idiff left right">9101630303384 0.2689168565046722 0.005172980464989402</span></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="plaintext">26 1.<span class="idiff left right">883724016460931e-07 0.09287622280393867 0.9071235888236596</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="plaintext">27 0.58<span class="idiff left right">96752507993037 0.3809199870370982 0.02940476216359821</span></span>
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287
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="plaintext">28 7.<span class="idiff left right">593295246048614e-14 0.0007914383645691474 0.999208561635355</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="plaintext">29 0.905<span class="idiff left right">5057132759483 0.09441475725209994 7.95294719517693</span>1e-05</span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="plaintext">30 0.47<span class="idiff left right">15021983865639 0.437031098794566 0.09146670281887008</span></span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="plaintext">31 0.00019<span class="idiff left right">79673775266633 0.4298989878010734 0.5699030448214001</span></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="plaintext">32 0.70<span class="idiff left right">1299413788691 0.2917569503013152 0.006943635909993886</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="plaintext">33 0.819<span class="idiff left right">4140603392319 0.1796652296204631 0.0009207100403048468</span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="plaintext">34 0.29<span class="idiff left right">60737907520586 0.6994108450666394 0.004515364181301996</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="plaintext">35 0.35<span class="idiff left right">59604560803941 0.641988793260765 0.002050750658840959</span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="plaintext">36 0.001<span class="idiff left right">30942674258278 0.8934690314170927 0.1052215418403245</span></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="plaintext">37 0.011<span class="idiff left right">80978530471919 0.9021622904359465 0.08602792425933428</span></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="plaintext">38 0.29<span class="idiff left right">41041942604504 0.7004973263923493 0.00539847934720022</span>6</span>
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="plaintext">39 0.0001<span class="idiff left right">44144499790302 0.3558514471530856 0.6440044083471241</span></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="plaintext">40 0.0002<span class="idiff left right">529699651473707 0.5439158494238194 0.4558311806110331</span></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="plaintext">41 0.2<span class="idiff left right">120674596489594 0.7760798923706854 0.01185264798035508</span></span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="plaintext">42 0.<span class="idiff left right">7007026627516525 0.2924393477253602 0.006857989522987185</span></span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="plaintext">43 0.48<span class="idiff left right">41294396612101 0.432198077596047 0.08367248274274289</span></span>
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="plaintext">44 0.0<span class="idiff left right">301228872990572 0.9580405078359099 0.0118366048650329</span>3</span>
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="plaintext">45 0.18<span class="idiff left right">93248839788894 0.7931688778993868 0.01750623812172373</span></span>
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="plaintext">46 0.003<span class="idiff left right">359794088751816 0.5672274449584306 0.4294127609528174</span></span>
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="plaintext">47 0.6<span class="idiff left right">3009891120623 0.3515230881722035 0.0183780006215666</span></span>
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="plaintext">48 0.02<span class="idiff left right">206748041476434 0.9525836698066102 0.02534884977862542</span></span>
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308
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="plaintext">49 0.013<span class="idiff left right">56591438428317 0.9153066291745316 0.0711274564411852</span>5</span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="plaintext">50 0.22<span class="idiff left right">40745276745924 0.7652910993933291 0.01063437293207849</span></span>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="plaintext">51 2.<span class="idiff left right">492645830161824e-08 0.1138985168648641 0.8861014582086777</span></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="plaintext">52 0.882<span class="idiff left right">2191864215847 0.1175582554811163 0.0002225580972989534</span></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="plaintext">53 0.82<span class="idiff left right">11660693180184 0.1780655702426055 0.0007683604393760527</span></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="plaintext">54 0.01<span class="idiff left right">100295212811388 0.8906447613794071 0.09835228649247904</span></span>
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314
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="plaintext">55 0.28<span class="idiff left right">33340811759865 0.7103263732591142 0.006339545564899368</span></span>
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315
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="plaintext">56 0.905<span class="idiff left right">5057132759483 0.09441475725209994 7.95294719517693</span>1e-05</span>
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316
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="plaintext">57 0.00<span class="idiff left right">7045975624482142 0.7878804894327445 0.2050735349427733</span></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="plaintext">58 0.82<span class="idiff left right">40613622898397 0.1752111065414368 0.000727531168723411</span></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="plaintext">59 0.004<span class="idiff left right">581163540158042 0.6639752834793526 0.3314435529804894</span></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="plaintext">60 0.58<span class="idiff left right">96752507993037 0.3809199870370982 0.02940476216359821</span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="plaintext">61 0.10<span class="idiff left right">7806169745878 0.8101927135133216 0.08200111674080049</span></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="plaintext">62 0.06<span class="idiff left right">861334373069095 0.7377206297197041 0.193666026549605</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="plaintext">63 0.012<span class="idiff left right">42704838986371 0.9103215529754771 0.0772513986346591</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="plaintext">64 0.023<span class="idiff left right">90636440935269 0.9546094186710312 0.02148421691961612</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="plaintext">65 0.02<span class="idiff left right">151934533944069 0.9510277882954953 0.02745286636506417</span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="plaintext">66 2.<span class="idiff left right">671166083534726e-12 0.001517686866166226 0.9984823131311625</span></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="plaintext">67 0.42<span class="idiff left right">95450384222473 0.4442725968259071 0.1261823647518457</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="plaintext">68 <span class="idiff left right">3.079998533959148e-05 0.3944141398788535 0.605555060135807</span></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="plaintext">69 <span class="idiff left right">4.243743084525438e-07 0.1666422297263941 0.8333573458992974</span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="plaintext">70 0.12<span class="idiff left right">88881665397853 0.8157663699880722 0.05534546347214257</span></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="plaintext">71 0.08<span class="idiff left right">913564852994389 0.7880791269944257 0.1227852244756305</span></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="plaintext">72 0.024<span class="idiff left right">99602234463322 0.9538989055654777 0.02110507208988902</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="plaintext">73 0.05<span class="idiff left right">300541149090041 0.6693935635419703 0.277601024967129</span>3</span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="plaintext">74 0.845<span class="idiff left right">4805150711112 0.1540601357267516 0.0004593492021371499</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="plaintext">75 0.004<span class="idiff left right">981355134669857 0.687674094236646 0.3073445506286841</span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="plaintext">76 1.<span class="idiff left right">275841252079727e-06 0.3240141526912666 0.6759845714674814</span></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="plaintext">77 0.888<span class="idiff left right">3601983297144 0.1114092796932183 0.0002305219770671781</span></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="plaintext">78 0.64<span class="idiff left right">85688357833093 0.3364376246912923 0.01499353952539858</span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="plaintext">79 0.3<span class="idiff left right">321969903648257 0.6645777090928409 0.003225300542333516</span></span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="plaintext">80 0.887<span class="idiff left right">4735538558555 0.112375266611063 0.0001511795330813065</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="plaintext">81 0.71<span class="idiff left right">93517468744175 0.2754744374209876 0.005173815704594973</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="plaintext">82 0.631<span class="idiff left right">9797015005985 0.3502496321154693 0.01777066638393202</span></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="plaintext">83 <span class="idiff left right">9.451297855017863e-07 0.1857524199000273 0.8142466349701873</span></span>
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343
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="plaintext">84 9.<span class="idiff left right">483309866743794e-05 0.7215660287271692 0.2783391381741632</span></span>
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344
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="plaintext">85 0.880<span class="idiff left right">7566499603399 0.119046866631502 0.0001964834081581603</span></span>
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345
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="plaintext">86 0.882<span class="idiff left right">2191864215847 0.1175582554811163 0.0002225580972989534</span></span>
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346
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="plaintext">87 1.<span class="idiff left right">512672292179054e-08 0.01436080404814105 0.985639180825136</span></span>
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347
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="plaintext">88 0.631<span class="idiff left right">9797015005985 0.3502496321154693 0.01777066638393202</span></span>
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348
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="plaintext">89 0.811<span class="idiff left right">7475469052963 0.1870790581657977 0.001173394928906147</span></span>
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349
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="plaintext">90 0.007<span class="idiff left right">483970311633406 0.8060983721720208 0.1864176575163458</span></span>
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350
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="plaintext">91 0.47<span class="idiff left right">58571278249646 0.4358530605425494 0.08828981163248605</span></span></pre>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext">Rate/Site Rate=0.05<span class="idiff left right">768869986246565 Rate=1 Rate=3.641844577696067</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext">1 2.<span class="idiff left right">014182872779183e-05 0.4994149475171328 0.5005649106541394</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext">2 0.845<span class="idiff left right">2194549572273 0.1543298717317663 0.0004506733110064033</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext">3 0.71<span class="idiff left right">64617500753068 0.2777040581733731 0.005834191751320087</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext">4 0.902<span class="idiff left right">2505078903756 0.09765491830787378 9.457380175062416</span>e-05</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext">5 0.58<span class="idiff left right">18848042477683 0.3867300951522449 0.03138510059998675</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext">6 0.887<span class="idiff left right">3636945850181 0.112488266098005 0.0001480393169770257</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext">7 0.70<span class="idiff left right">05076792958981 0.2926448925794821 0.006847428124619753</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext">8 0.52<span class="idiff left right">47883329162988 0.4190151125074336 0.05619655457626769</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext">9 0.0010<span class="idiff left right">25124165060435 0.2787132641689699 0.7202616116659697</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext">10 0.<span class="idiff left right">0988666787453516 0.8058113455742041 0.09532197568044432</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext">11 0.819<span class="idiff left right">0555318482564 0.1800397947137043 0.0009046734380393297</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext">12 0.67<span class="idiff left right">08961696125029 0.3186015906223785 0.01050223976511856</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext">13 0.864<span class="idiff left right">433000690832 0.1350822406375951 0.0004847586715730755</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext">14 0.56<span class="idiff left right">13826888688731 0.399110465915229 0.03950684521589812</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext">15 0.882<span class="idiff left right">0922333215474 0.117689551078845 0.0002182155996077391</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext">16 0.882<span class="idiff left right">0922333215474 0.117689551078845 0.0002182155996077391</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext">17 0.845<span class="idiff left right">2194549572273 0.1543298717317663 0.0004506733110064033</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext">18 0.032<span class="idiff left right">4851386885853 0.537132150947249 0.4303827103641656</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="plaintext">19 0.66<span class="idiff left right">36954012888419 0.3248421264843285 0.01146247222682962</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext">20 0.15<span class="idiff left right">74210003780902 0.8093916351273479 0.03318736449456186</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext">21 6.<span class="idiff left right">147404749371294e-05 0.7563030265731285 0.2436354993793777</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext">22 <span class="idiff left right">5.912803676264833e-05 0.2036709233466827 0.7962699486165546</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext">23 0.845<span class="idiff left right">2194549572273 0.1543298717317663 0.0004506733110064033</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="plaintext">24 1.<span class="idiff left right">697882291310795e-06 0.4205871212739687 0.57941118084374</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext">25 0.725<span class="idiff left right">2007199820658 0.2696995518527805 0.005099728165153801</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext">26 1.<span class="idiff left right">76903184809418e-07 0.09425089041459019 0.905748932682225</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext">27 0.58<span class="idiff left right">86393930203893 0.3822786807540463 0.02908192622556446</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="plaintext">28 7.<span class="idiff left right">257830102405714e-14 0.000810598559615294 0.9991894014403121</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext">29 0.905<span class="idiff left right">453981684754 0.09446823634507101 7.77819701749575</span>1e-05</span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext">30 0.47<span class="idiff left right">04804321322921 0.438821028210632 0.09069853965707597</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="plaintext">31 0.00019<span class="idiff left right">0267409636111 0.4337695463035081 0.5660401862868557</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext">32 0.70<span class="idiff left right">05076792958981 0.2926448925794821 0.006847428124619753</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext">33 0.819<span class="idiff left right">0555318482564 0.1800397947137043 0.0009046734380393297</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext">34 0.29<span class="idiff left right">27441515249551 0.7028130343101993 0.004442814164845603</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext">35 0.35<span class="idiff left right">24412830671291 0.6455423115099926 0.002016405422878198</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext">36 0.001<span class="idiff left right">253859115858844 0.895365459904557 0.1033806809795843</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext">37 0.011<span class="idiff left right">45549195170351 0.9039575344632091 0.0845869735850874</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext">38 0.29<span class="idiff left right">07971110003181 0.7038873198822431 0.00531556911743883</span>6</span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext">39 0.0001<span class="idiff left right">386157668289592 0.3593650200992473 0.6404963641339237</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext">40 0.0002<span class="idiff left right">432878779577585 0.5484344029384893 0.4513223091835529</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext">41 0.2<span class="idiff left right">092473563395368 0.7790901204293758 0.01166252323108743</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext">42 0.<span class="idiff left right">6999063654856726 0.2933310736890647 0.006762560825262604</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext">43 0.48<span class="idiff left right">31185953460878 0.4339365100258424 0.08294489462806978</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext">44 0.0<span class="idiff left right">292576800605162 0.9591508668397269 0.0115914530997568</span>3</span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext">45 0.18<span class="idiff left right">67006668711101 0.796065293589396 0.01723403953949377</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext">46 0.003<span class="idiff left right">266315231745858 0.5708537790812774 0.4258799056869767</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext">47 0.6<span class="idiff left right">291274207544222 0.3527143572968038 0.01815822194877413</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext">48 0.02<span class="idiff left right">141713714322223 0.9537233271429686 0.0248595357138091</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext">49 0.013<span class="idiff left right">17171754156796 0.9169778943953281 0.0698503880631039</span>5</span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext">50 0.22<span class="idiff left right">11497254419244 0.7683821429887575 0.01046813156931801</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext">51 2.<span class="idiff left right">314690514493323e-08 0.11579905354917 0.8842009233039249</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext">52 0.882<span class="idiff left right">0922333215474 0.117689551078845 0.0002182155996077391</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext">53 0.82<span class="idiff left right">08101360851635 0.1784353736120698 0.0007544903027667682</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext">54 0.01<span class="idiff left right">067202582008938 0.8925634355906562 0.09676453858925446</span></span>
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<td class="diff-line-num new new_line" 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">
314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext">55 0.28<span class="idiff left right">00657198062314 0.7136903078243987 0.006243972369370006</span></span>
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<td class="diff-line-num new new_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="plaintext">56 0.905<span class="idiff left right">453981684754 0.09446823634507101 7.77819701749575</span>1e-05</span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="plaintext">57 0.00<span class="idiff left right">6838110356898206 0.7907443614840988 0.2024175281590031</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="plaintext">58 0.82<span class="idiff left right">37175911135334 0.1755680757274284 0.0007143331590382112</span></span>
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<td class="diff-line-num new new_line" 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">
318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="plaintext">59 0.004<span class="idiff left right">450345634491975 0.6674673518063451 0.328082302559163</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext">60 0.58<span class="idiff left right">86393930203893 0.3822786807540463 0.02908192622556446</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="plaintext">61 0.10<span class="idiff left right">61213208343808 0.812930108584915 0.08094857058070434</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext">62 0.06<span class="idiff left right">753143245596548 0.7407839653331104 0.191684602210924</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext">63 0.012<span class="idiff left right">05277332437679 0.9120050156770158 0.07594221099860735</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext">64 0.023<span class="idiff left right">20619483438383 0.9557274248346076 0.02106638033100854</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext">65 0.02<span class="idiff left right">088692244142688 0.952186701680194 0.02692637587837913</span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext">66 2.<span class="idiff left right">448383399924293e-12 0.001541519148066872 0.9984584808494847</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="plaintext">67 0.42<span class="idiff left right">85837636617972 0.4461870784691586 0.1252291578690442</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext">68 <span class="idiff left right">2.946025360697879e-05 0.3986390642624525 0.6013314754839405</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="plaintext">69 <span class="idiff left right">3.98203585590263e-07 0.1689738383946639 0.8310257634017505</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="plaintext">70 0.12<span class="idiff left right">69233311499915 0.8184808528260092 0.05459581602399919</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="plaintext">71 0.08<span class="idiff left right">772963484839656 0.7909364230012607 0.1213339421503428</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="plaintext">72 0.024<span class="idiff left right">26486820361876 0.9550309540228338 0.02070417777354739</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="plaintext">73 0.05<span class="idiff left right">217899891051785 0.6725979338073078 0.275223067282174</span>3</span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext">74 0.845<span class="idiff left right">2194549572273 0.1543298717317663 0.0004506733110064033</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="plaintext">75 0.004<span class="idiff left right">838241899341649 0.6910808908987468 0.3040808672019115</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="plaintext">76 1.<span class="idiff left right">198920235239551e-06 0.3283198816772326 0.6716789194025321</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="plaintext">77 0.888<span class="idiff left right">2667916649903 0.1115071478917882 0.0002260604432214562</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="plaintext">78 0.64<span class="idiff left right">76389301739991 0.337551894066365 0.01480917575963592</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="plaintext">79 0.3<span class="idiff left right">286907698848671 0.668133669737322 0.003175560377811062</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="plaintext">80 0.887<span class="idiff left right">3636945850181 0.112488266098005 0.0001480393169770257</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="plaintext">81 0.71<span class="idiff left right">86192824913594 0.2762818662060978 0.005098851302542715</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="plaintext">82 0.631<span class="idiff left right">00855429723 0.3514345786959893 0.01755686700678069</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="plaintext">83 <span class="idiff left right">8.934097890872577e-07 0.1882942394050127 0.8117048671851982</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="plaintext">84 9.<span class="idiff left right">275585147221103e-05 0.725714033089126 0.2741932110594019</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="plaintext">85 0.880<span class="idiff left right">6249498392179 0.1191825284490111 0.0001925217117709219</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="plaintext">86 0.882<span class="idiff left right">0922333215474 0.117689551078845 0.0002182155996077391</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="plaintext">87 1.<span class="idiff left right">429077450481847e-08 0.0145433538421707 0.9854566318670548</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="plaintext">88 0.631<span class="idiff left right">00855429723 0.3514345786959893 0.01755686700678069</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="plaintext">89 0.811<span class="idiff left right">3577821477324 0.1874886460858839 0.001153571766383773</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="plaintext">90 0.007<span class="idiff left right">262246700933957 0.8088313705080076 0.1839063827910584</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="plaintext">91 0.47<span class="idiff left right">48305935897082 0.4376288899812887 0.0875405164290031</span></span></pre>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/e5c8fd32984d059ec09233aa8f7e5cdb888c538c#3bbc19efb5ab1243a9d0c4627a24ef88cf1f3ca0"><strong>tests/hbltests/Results/HIVSweden.out_MODEL_-1.nex</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">@@ -37,8 +37,8 @@ END;</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">BEGIN HYPHY;</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">global c=0.90<span class="idiff left right">51395450601901</span>;</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">global kappa=0.405<span class="idiff left right">2422178470169</span>;</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">global c=0.90<span class="idiff left right">71719918589423</span>;</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">global kappa=0.405<span class="idiff left right">4779971121202</span>;</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">modelMatrix={61,61};</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">modelMatrix[0][1]:=kappa*c*t;</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">modelMatrix[0][2]:=t;</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">@@ -636,33 +636,35 @@ TRY_NUMERIC_SEQUENCE_MATCH=0;</td>
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="plaintext">ACCEPT_ROOTED_TREES=0;</span>
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="plaintext">UseModel (theModel);</span>
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<pre style="margin: 0;">-<span id="LC639" class="line" lang="plaintext">Tree givenTree=(((U68496,U68497)Node3,(U68501,(U68502,(U68503,((((U68504,U68506)Node15,U68505)Node14,U68507)Node13,U68508)Node12)Node10)Node8)Node6)Node2,U68498,(U68499,U68500)Node6_1);</span>
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="plaintext">Tree givenTree=(U68496,U68497,((U68498,(U68499,U68500)Node7)Node5,(U68501,(U68502,(U68503,((((U68504,U68506)Node19,U68505)Node18,U68507)Node17,U68508)Node16)Node14)Node12)Node10)Node4);</span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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">
641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="plaintext">givenTree.U68496.t=0.1930890973257582;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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">
642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="plaintext">givenTree.U68497.t=0.6424612223788787;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="plaintext">givenTree.U68498.t=0.409121209278724;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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">
644
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="plaintext">givenTree.U68499.t=0.2307021519626118;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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">
645
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="plaintext">givenTree.U68500.t=0.8109768825230198;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="plaintext">givenTree.Node7.t=0.6770911492487591;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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">
647
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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="plaintext">givenTree.Node5.t=0.192056403882526;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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">
648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="plaintext">givenTree.U68501.t=1.068413022713992;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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">
649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="plaintext">givenTree.U68502.t=1.553405763007259;</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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">
650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="plaintext">givenTree.U68503.t=1.569000404650932;</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="plaintext">givenTree.U68504.t=0.1542179615342612;</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="plaintext">givenTree.U68506.t=0.5708195775387649;</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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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<pre style="margin: 0;">+<span id="LC653" class="line" lang="plaintext">givenTree.Node19.t=0.4514474490820354;</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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="plaintext">givenTree.U68505.t=0.2461875505020575;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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="plaintext">givenTree.Node18.t=0.2979766094476649;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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
</td>
<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="plaintext">givenTree.U68507.t=0.4958919610910434;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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
</td>
<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="plaintext">givenTree.Node17.t=0.2823906966108597;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" 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
</td>
<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="plaintext">givenTree.U68508.t=1.611576611031497;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" 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="plaintext">givenTree.Node16.t=0.4108260863152219;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" 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="plaintext">givenTree.Node14.t=0.5198983543648987;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" 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="plaintext">givenTree.Node12.t=0.2732130787806588;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" 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="plaintext">givenTree.Node10.t=0.3908328965048091;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" 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
</td>
<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="plaintext">givenTree.Node4.t=1.241058558313147;SetParameter (DEFER_CONSTRAINT_APPLICATION, 1, 0);</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" 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
</td>
<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="plaintext">SetParameter (DEFER_CONSTRAINT_APPLICATION, 0, 0);</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
640
</td>
<td class="diff-line-num new_line" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
665
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC641" class="line" lang="plaintext">givenTree.U68496.t=0.1932757790297635;</span>
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<pre style="margin: 0;">-<span id="LC642" class="line" lang="plaintext">givenTree.U68497.t=0.6442091360697517;</span>
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<pre style="margin: 0;">-<span id="LC643" class="line" lang="plaintext">givenTree.Node3.t=1.244091350196699;</span>
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<pre style="margin: 0;">-<span id="LC644" class="line" lang="plaintext">givenTree.U68501.t=1.072314145612458;</span>
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<pre style="margin: 0;">-<span id="LC645" class="line" lang="plaintext">givenTree.U68502.t=1.555368999549274;</span>
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<pre style="margin: 0;">-<span id="LC646" class="line" lang="plaintext">givenTree.U68503.t=1.573795636757062;</span>
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<pre style="margin: 0;">-<span id="LC647" class="line" lang="plaintext">givenTree.U68504.t=0.1545017778755618;</span>
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<pre style="margin: 0;">-<span id="LC648" class="line" lang="plaintext">givenTree.U68506.t=0.5724438957384254;</span>
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<pre style="margin: 0;">-<span id="LC649" class="line" lang="plaintext">givenTree.Node15.t=0.452076415208067;</span>
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<pre style="margin: 0;">-<span id="LC650" class="line" lang="plaintext">givenTree.U68505.t=0.2464768693858635;</span>
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<pre style="margin: 0;">-<span id="LC651" class="line" lang="plaintext">givenTree.Node14.t=0.2982771493845721;</span>
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<pre style="margin: 0;">-<span id="LC652" class="line" lang="plaintext">givenTree.U68507.t=0.4974360955659346;</span>
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="plaintext">givenTree.Node13.t=0.2831885574728508;</span>
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<pre style="margin: 0;">-<span id="LC654" class="line" lang="plaintext">givenTree.U68508.t=1.613919861191977;</span>
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<pre style="margin: 0;">-<span id="LC655" class="line" lang="plaintext">givenTree.Node12.t=0.41156092487671;</span>
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="plaintext">givenTree.Node10.t=0.5209728334125625;</span>
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="plaintext">givenTree.Node8.t=0.2739993974710216;</span>
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<pre style="margin: 0;">-<span id="LC658" class="line" lang="plaintext">givenTree.Node6.t=0.3910850502827137;</span>
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<td class="diff-line-num old old_line" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC659" class="line" lang="plaintext">givenTree.Node2.t=0.1922077082389846;</span>
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<pre style="margin: 0;">-<span id="LC660" class="line" lang="plaintext">givenTree.U68498.t=0.4102499738247144;</span>
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="plaintext">givenTree.U68499.t=0.2311741894617957;</span>
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<pre style="margin: 0;">-<span id="LC662" class="line" lang="plaintext">givenTree.U68500.t=0.8119659118420136;</span>
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663
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="plaintext">givenTree.Node6_1.t=0.678816471820221;</span>
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664
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666
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="plaintext">DataSet ds = ReadDataFile(USE_NEXUS_FILE_DATA);</span>
</pre>
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665
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<pre style="margin: 0;">-<span id="LC665" class="line" lang="plaintext">DataSetFilter filteredData = CreateFilter(ds,3,"0-272","0<span class="idiff left right">,1,5-8,10,9,11,12,2-4</span>","TAA,TAG,TGA");</span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="plaintext">DataSetFilter filteredData = CreateFilter(ds,3,"0-272","0<span class="idiff left right">-8,10,9,11,12</span>","TAA,TAG,TGA");</span>
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="plaintext">ASSUME_REVERSIBLE_MODELS=0;</span>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="plaintext">USE_LAST_RESULTS=1;</span>
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="plaintext">LikelihoodFunction lf = (filteredData,givenTree);</span>
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<li id="96e4cef3847de919b0f245e8443e6befe26c217b">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/e5c8fd32984d059ec09233aa8f7e5cdb888c538c#96e4cef3847de919b0f245e8443e6befe26c217b"><strong>tests/hbltests/Results/HIVSweden.out_MODEL_0.nex</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">@@ -37,11 +37,11 @@ END;</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">BEGIN HYPHY;</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">global W=0.078<span class="idiff left right">54089951899505</span>;</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">global W=0.078<span class="idiff left right">48544796897376</span>;</span>
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">W:<1;</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">global P=0.4830<span class="idiff left right">17317295036</span>;</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">global P=0.4830<span class="idiff left right">911811352628</span>;</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">P:<1;</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext">global kappa=0.386<span class="idiff left right">391531490961</span>2;</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">global kappa=0.386<span class="idiff left right">257210859582</span>2;</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">c.weights={1,2};</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">c.weights[0][0]:=P;</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">@@ -652,33 +652,35 @@ TRY_NUMERIC_SEQUENCE_MATCH=0;</td>
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<pre style="margin: 0;"> <span id="LC652" class="line" lang="plaintext">ACCEPT_ROOTED_TREES=0;</span>
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<pre style="margin: 0;"> <span id="LC653" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC654" class="line" lang="plaintext">UseModel (theModel);</span>
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<pre style="margin: 0;">-<span id="LC655" class="line" lang="plaintext">Tree givenTree=(((U68496,U68497)Node3,(U68501,(U68502,(U68503,((((U68504,U68506)Node15,U68505)Node14,U68507)Node13,U68508)Node12)Node10)Node8)Node6)Node2,U68498,(U68499,U68500)Node6_1);</span>
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="plaintext">Tree givenTree=(U68496,U68497,((U68498,(U68499,U68500)Node7)Node5,(U68501,(U68502,(U68503,((((U68504,U68506)Node19,U68505)Node18,U68507)Node17,U68508)Node16)Node14)Node12)Node10)Node4);</span>
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656
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="plaintext"></span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="plaintext">givenTree.U68496.t=0.3017206887153597;</span>
</pre>
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<td class="diff-line-num new old_line" 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">
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC658" class="line" lang="plaintext">givenTree.U68497.t=1.059711785366983;</span>
</pre>
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<td class="diff-line-num new old_line" 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">
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC659" class="line" lang="plaintext">givenTree.U68498.t=0.6389397418529784;</span>
</pre>
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<td class="diff-line-num new old_line" 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">
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC660" class="line" lang="plaintext">givenTree.U68499.t=0.3596540096621793;</span>
</pre>
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<td class="diff-line-num new old_line" 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">
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC661" class="line" lang="plaintext">givenTree.U68500.t=1.321906771217612;</span>
</pre>
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<td class="diff-line-num new old_line" 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">
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC662" class="line" lang="plaintext">givenTree.Node7.t=1.136554744000134;</span>
</pre>
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<td class="diff-line-num new old_line" 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">
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC663" class="line" lang="plaintext">givenTree.Node5.t=0.3043513200848355;</span>
</pre>
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<td class="diff-line-num new old_line" 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">
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC664" class="line" lang="plaintext">givenTree.U68501.t=1.769569624859784;</span>
</pre>
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<td class="diff-line-num new old_line" 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">
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC665" class="line" lang="plaintext">givenTree.U68502.t=2.675115127943899;</span>
</pre>
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<td class="diff-line-num new old_line" 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">
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="plaintext">givenTree.U68503.t=2.706643713132597;</span>
</pre>
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<td class="diff-line-num new old_line" 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">
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="plaintext">givenTree.U68504.t=0.2431327474261901;</span>
</pre>
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<td class="diff-line-num new old_line" 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">
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="plaintext">givenTree.U68506.t=0.9044122018972757;</span>
</pre>
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<td class="diff-line-num new old_line" 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">
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<td class="diff-line-num new new_line" 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>
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="plaintext">givenTree.Node19.t=0.7162910919155517;</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" 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">
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC670" class="line" lang="plaintext">givenTree.U68505.t=0.3956882184714828;</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" 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">
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<td class="diff-line-num new new_line" 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="plaintext">givenTree.Node18.t=0.4996707175132051;</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" 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">
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<td class="diff-line-num new new_line" 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="plaintext">givenTree.U68507.t=0.774075369790494;</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" 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">
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<td class="diff-line-num new new_line" 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="plaintext">givenTree.Node17.t=0.2764202496369115;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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">
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<td class="diff-line-num new new_line" 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="plaintext">givenTree.U68508.t=2.852778762374758;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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">
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<td class="diff-line-num new new_line" 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
</td>
<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="plaintext">givenTree.Node16.t=0.7482651562390982;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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">
</td>
<td class="diff-line-num new new_line" 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="plaintext">givenTree.Node14.t=0.8229119584835572;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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">
</td>
<td class="diff-line-num new new_line" 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
</td>
<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="plaintext">givenTree.Node12.t=0.3096780975715163;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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">
</td>
<td class="diff-line-num new new_line" 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="plaintext">givenTree.Node10.t=0.6408915003259278;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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">
</td>
<td class="diff-line-num new new_line" 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
</td>
<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="plaintext">givenTree.Node4.t=2.084190034363844;SetParameter (DEFER_CONSTRAINT_APPLICATION, 1, 0);</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
680
</td>
<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="plaintext">SetParameter (DEFER_CONSTRAINT_APPLICATION, 0, 0);</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
656
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681
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<pre style="margin: 0;"> <span id="LC681" class="line" lang="plaintext"></span>
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657
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="plaintext">givenTree.U68496.t=0.3014658876783538;</span>
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658
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<pre style="margin: 0;">-<span id="LC658" class="line" lang="plaintext">givenTree.U68497.t=1.058937965054783;</span>
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<td class="diff-line-num old old_line" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
659
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<pre style="margin: 0;">-<span id="LC659" class="line" lang="plaintext">givenTree.Node3.t=2.08174984846752;</span>
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<td class="diff-line-num old old_line" 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
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<pre style="margin: 0;">-<span id="LC660" class="line" lang="plaintext">givenTree.U68501.t=1.764333870286974;</span>
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<td class="diff-line-num old old_line" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
661
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="plaintext">givenTree.U68502.t=2.673570567299918;</span>
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<td class="diff-line-num old old_line" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
662
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<pre style="margin: 0;">-<span id="LC662" class="line" lang="plaintext">givenTree.U68503.t=2.699658069558426;</span>
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663
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="plaintext">givenTree.U68504.t=0.2431541588198822;</span>
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<td class="diff-line-num old old_line" data-linenumber="664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
664
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<pre style="margin: 0;">-<span id="LC664" class="line" lang="plaintext">givenTree.U68506.t=0.9038084521967604;</span>
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665
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<pre style="margin: 0;">-<span id="LC665" class="line" lang="plaintext">givenTree.Node15.t=0.7153498168088975;</span>
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666
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<pre style="margin: 0;">-<span id="LC666" class="line" lang="plaintext">givenTree.U68505.t=0.3956539001874164;</span>
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<td class="diff-line-num old old_line" data-linenumber="667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
667
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<pre style="margin: 0;">-<span id="LC667" class="line" lang="plaintext">givenTree.Node14.t=0.4993402949067045;</span>
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<td class="diff-line-num old old_line" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
668
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<pre style="margin: 0;">-<span id="LC668" class="line" lang="plaintext">givenTree.U68507.t=0.7737346315034068;</span>
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<td class="diff-line-num old old_line" data-linenumber="669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
669
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<pre style="margin: 0;">-<span id="LC669" class="line" lang="plaintext">givenTree.Node13.t=0.277145717534158;</span>
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670
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<pre style="margin: 0;">-<span id="LC670" class="line" lang="plaintext">givenTree.U68508.t=2.851718049074558;</span>
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671
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<pre style="margin: 0;">-<span id="LC671" class="line" lang="plaintext">givenTree.Node12.t=0.7478267266145866;</span>
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672
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<pre style="margin: 0;">-<span id="LC672" class="line" lang="plaintext">givenTree.Node10.t=0.8232048503168657;</span>
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<td class="diff-line-num old old_line" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
673
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<pre style="margin: 0;">-<span id="LC673" class="line" lang="plaintext">givenTree.Node8.t=0.309357412100375;</span>
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674
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<pre style="margin: 0;">-<span id="LC674" class="line" lang="plaintext">givenTree.Node6.t=0.6402997546627597;</span>
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<td class="diff-line-num old old_line" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
675
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<pre style="margin: 0;">-<span id="LC675" class="line" lang="plaintext">givenTree.Node2.t=0.3042887273137687;</span>
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676
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<pre style="margin: 0;">-<span id="LC676" class="line" lang="plaintext">givenTree.U68498.t=0.6387909451494354;</span>
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677
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<pre style="margin: 0;">-<span id="LC677" class="line" lang="plaintext">givenTree.U68499.t=0.3594052835330087;</span>
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<td class="diff-line-num old old_line" data-linenumber="678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
678
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<pre style="margin: 0;">-<span id="LC678" class="line" lang="plaintext">givenTree.U68500.t=1.319979691408115;</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
679
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<pre style="margin: 0;">-<span id="LC679" class="line" lang="plaintext">givenTree.Node6_1.t=1.13804766964687;</span>
</pre>
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680
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682
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<pre style="margin: 0;"> <span id="LC682" class="line" lang="plaintext">DataSet ds = ReadDataFile(USE_NEXUS_FILE_DATA);</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
681
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<td class="diff-line-num new_line old" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC681" class="line" lang="plaintext">DataSetFilter filteredData = CreateFilter(ds,3,"0-272","0<span class="idiff left right">,1,5-8,10,9,11,12,2-4</span>","TAA,TAG,TGA");</span>
</pre>
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="plaintext">DataSetFilter filteredData = CreateFilter(ds,3,"0-272","0<span class="idiff left right">-8,10,9,11,12</span>","TAA,TAG,TGA");</span>
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<pre style="margin: 0;"> <span id="LC684" class="line" lang="plaintext">ASSUME_REVERSIBLE_MODELS=0;</span>
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<pre style="margin: 0;"> <span id="LC685" class="line" lang="plaintext">USE_LAST_RESULTS=1;</span>
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<pre style="margin: 0;"> <span id="LC686" class="line" lang="plaintext">LikelihoodFunction lf = (filteredData,givenTree);</span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/e5c8fd32984d059ec09233aa8f7e5cdb888c538c#dc4367ca74d002d80f8b7061c05e7d0232904a74"><strong>tests/hbltests/Results/HIVSweden.out_MODEL_1.nex</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">@@ -37,15 +37,15 @@ END;</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">BEGIN HYPHY;</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">global P2=0.7<span class="idiff left right">081253811493516</span>;</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">global P2=0.7<span class="idiff left right">104121522639678</span>;</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">P2:<1;</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">global W_1=0.05<span class="idiff left right">854805862606752</span>;</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">global W_1=0.05<span class="idiff left right">768869986246565</span>;</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">W_1:<1;</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext">global W_2=3.64<span class="idiff left right">0709855148721</span>;</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">global W_2=3.64<span class="idiff left right">1844577696067</span>;</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">W_2:>1;</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">global P1=0.37<span class="idiff left right">47723001916182</span>;</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">global P1=0.37<span class="idiff left right">39141342952348</span>;</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">P1:<1;</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext">global kappa=0.3597<span class="idiff left right">040016204291</span>;</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">global kappa=0.3597<span class="idiff left right">183898000834</span>;</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">c.weights={1,3};</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">c.weights[0][0]:=P1;</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">@@ -658,33 +658,35 @@ TRY_NUMERIC_SEQUENCE_MATCH=0;</td>
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658
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658
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="plaintext">ACCEPT_ROOTED_TREES=0;</span>
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659
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659
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<pre style="margin: 0;"> <span id="LC659" class="line" lang="plaintext"></span>
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660
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660
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="plaintext">UseModel (theModel);</span>
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661
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="plaintext">Tree givenTree=(((U68496,U68497)Node3,(U68501,(U68502,(U68503,((((U68504,U68506)Node15,U68505)Node14,U68507)Node13,U68508)Node12)Node10)Node8)Node6)Node2,U68498,(U68499,U68500)Node6_1);</span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="plaintext">Tree givenTree=(U68496,U68497,((U68498,(U68499,U68500)Node7)Node5,(U68501,(U68502,(U68503,((((U68504,U68506)Node19,U68505)Node18,U68507)Node17,U68508)Node16)Node14)Node12)Node10)Node4);</span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="plaintext"></span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="plaintext">givenTree.U68496.t=0.1820765235473329;</span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="plaintext">givenTree.U68497.t=0.6321073455214453;</span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="plaintext">givenTree.U68498.t=0.3343564501791256;</span>
</pre>
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<td class="diff-line-num new old_line" 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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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="plaintext">givenTree.U68499.t=0.1876640197504523;</span>
</pre>
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<td class="diff-line-num new old_line" 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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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="plaintext">givenTree.U68500.t=0.8005801879569905;</span>
</pre>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="plaintext">givenTree.Node7.t=0.750108304945318;</span>
</pre>
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<td class="diff-line-num new old_line" 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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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="plaintext">givenTree.Node5.t=0.189875002788432;</span>
</pre>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="plaintext">givenTree.U68501.t=1.055571283712865;</span>
</pre>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="plaintext">givenTree.U68502.t=1.747134065548263;</span>
</pre>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="plaintext">givenTree.U68503.t=1.779098089271837;</span>
</pre>
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<td class="diff-line-num new old_line" 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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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="plaintext">givenTree.U68504.t=0.1466122835681893;</span>
</pre>
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<td class="diff-line-num new old_line" 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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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="plaintext">givenTree.U68506.t=0.5212546540008767;</span>
</pre>
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<td class="diff-line-num new old_line" 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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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="plaintext">givenTree.Node19.t=0.4171959202637034;</span>
</pre>
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<td class="diff-line-num new old_line" 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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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="plaintext">givenTree.U68505.t=0.2414131900046768;</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" 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="plaintext">givenTree.Node18.t=0.2762126262689943;</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" 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="plaintext">givenTree.U68507.t=0.4784362608407944;</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" 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
</td>
<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="plaintext">givenTree.Node17.t=0.006818214720109361;</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
680
</td>
<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="plaintext">givenTree.U68508.t=1.945808887957573;</span>
</pre>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="plaintext">givenTree.Node16.t=0.5086054961633685;</span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="plaintext">givenTree.Node14.t=0.508023542650578;</span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="plaintext">givenTree.Node12.t=0.1816851776949857;</span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="plaintext">givenTree.Node10.t=0.394526379685196;</span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="plaintext">givenTree.Node4.t=1.247106653589127;SetParameter (DEFER_CONSTRAINT_APPLICATION, 1, 0);</span>
</pre>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="plaintext">SetParameter (DEFER_CONSTRAINT_APPLICATION, 0, 0);</span>
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662
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687
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<pre style="margin: 0;"> <span id="LC687" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
663
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<td class="diff-line-num new_line 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">
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="plaintext">givenTree.U68496.t=0.1819372645612003;</span>
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<td class="diff-line-num old old_line" data-linenumber="664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
664
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<td class="diff-line-num new_line 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">
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<pre style="margin: 0;">-<span id="LC664" class="line" lang="plaintext">givenTree.U68497.t=0.6305701510272947;</span>
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<td class="diff-line-num old old_line" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
665
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<pre style="margin: 0;">-<span id="LC665" class="line" lang="plaintext">givenTree.Node3.t=1.244260990073252;</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
666
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<pre style="margin: 0;">-<span id="LC666" class="line" lang="plaintext">givenTree.U68501.t=1.05208595250357;</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
667
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<pre style="margin: 0;">-<span id="LC667" class="line" lang="plaintext">givenTree.U68502.t=1.746445328113835;</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
668
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<pre style="margin: 0;">-<span id="LC668" class="line" lang="plaintext">givenTree.U68503.t=1.774938469552289;</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
669
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<td class="diff-line-num new_line 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">
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<pre style="margin: 0;">-<span id="LC669" class="line" lang="plaintext">givenTree.U68504.t=0.1463724860825859;</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
670
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<td class="diff-line-num new_line 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">
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<pre style="margin: 0;">-<span id="LC670" class="line" lang="plaintext">givenTree.U68506.t=0.5200057981767465;</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
671
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<td class="diff-line-num new_line 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">
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<pre style="margin: 0;">-<span id="LC671" class="line" lang="plaintext">givenTree.Node15.t=0.4166914000694648;</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
672
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<td class="diff-line-num new_line 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">
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<pre style="margin: 0;">-<span id="LC672" class="line" lang="plaintext">givenTree.U68505.t=0.241055361539026;</span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
673
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<td class="diff-line-num new_line 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">
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<pre style="margin: 0;">-<span id="LC673" class="line" lang="plaintext">givenTree.Node14.t=0.2754520695076969;</span>
</pre>
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</tr>
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<td class="diff-line-num old old_line" data-linenumber="674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
674
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<td class="diff-line-num new_line 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">
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<pre style="margin: 0;">-<span id="LC674" class="line" lang="plaintext">givenTree.U68507.t=0.4771824473110387;</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
675
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<td class="diff-line-num new_line 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">
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<pre style="margin: 0;">-<span id="LC675" class="line" lang="plaintext">givenTree.Node13.t=0.006305605103123437;</span>
</pre>
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<td class="diff-line-num old old_line" 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">
676
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<td class="diff-line-num new_line 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">
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<pre style="margin: 0;">-<span id="LC676" class="line" lang="plaintext">givenTree.U68508.t=1.944259154790765;</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
677
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<td class="diff-line-num new_line 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">
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<pre style="margin: 0;">-<span id="LC677" class="line" lang="plaintext">givenTree.Node12.t=0.5081406979260248;</span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
678
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<td class="diff-line-num new_line 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">
</td>
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<pre style="margin: 0;">-<span id="LC678" class="line" lang="plaintext">givenTree.Node10.t=0.5074584441922946;</span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
679
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<td class="diff-line-num new_line 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC679" class="line" lang="plaintext">givenTree.Node8.t=0.1808898503811754;</span>
</pre>
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</tr>
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<td class="diff-line-num old old_line" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
680
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<td class="diff-line-num new_line 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC680" class="line" lang="plaintext">givenTree.Node6.t=0.3939031724767187;</span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
681
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<pre style="margin: 0;">-<span id="LC681" class="line" lang="plaintext">givenTree.Node2.t=0.1896556393922262;</span>
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682
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<pre style="margin: 0;">-<span id="LC682" class="line" lang="plaintext">givenTree.U68498.t=0.3337924593752155;</span>
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683
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<pre style="margin: 0;">-<span id="LC683" class="line" lang="plaintext">givenTree.U68499.t=0.1875734352334583;</span>
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684
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<pre style="margin: 0;">-<span id="LC684" class="line" lang="plaintext">givenTree.U68500.t=0.7998185516002427;</span>
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685
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<pre style="margin: 0;">-<span id="LC685" class="line" lang="plaintext">givenTree.Node6_1.t=0.7492860788646263;</span>
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686
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688
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<pre style="margin: 0;"> <span id="LC688" class="line" lang="plaintext">DataSet ds = ReadDataFile(USE_NEXUS_FILE_DATA);</span>
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687
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<pre style="margin: 0;">-<span id="LC687" class="line" lang="plaintext">DataSetFilter filteredData = CreateFilter(ds,3,"0-272","0<span class="idiff left right">,1,5-8,10,9,11,12,2-4</span>","TAA,TAG,TGA");</span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="plaintext">DataSetFilter filteredData = CreateFilter(ds,3,"0-272","0<span class="idiff left right">-8,10,9,11,12</span>","TAA,TAG,TGA");</span>
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688
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690
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<pre style="margin: 0;"> <span id="LC690" class="line" lang="plaintext">ASSUME_REVERSIBLE_MODELS=0;</span>
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689
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691
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<pre style="margin: 0;"> <span id="LC691" class="line" lang="plaintext">USE_LAST_RESULTS=1;</span>
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690
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692
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="plaintext">LikelihoodFunction lf = (filteredData,givenTree);</span>
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