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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/d482898df35710ff14413712f36f8cac7cd945b5">d482898d</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-25T19:32:00+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.5.32+dfsg</pre>
</li>
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<h4>29 changed files:</h4>
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<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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<li class="file-stats">
<a href="#0570609ee9b4163f9738e06f4afb1114320867f5">
res/TemplateBatchFiles/AddABias.ibf
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<li class="file-stats">
<a href="#1c34e5e2341f7334d9146eb8e633fd86fdc01c3d">
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res/TemplateBatchFiles/DirectionalREL.bf
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<li class="file-stats">
<a href="#595b42362bc80e51259da598ac8ff2dd32cd7358">
res/TemplateBatchFiles/GARD.bf
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<li class="file-stats">
<a href="#4ed0809c2483f5150cdfd2c3bf07d212387406d0">
res/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf
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<li class="file-stats">
<a href="#f029f7293cd2f0d6999ed6bdfd41727a79f56162">
res/TemplateBatchFiles/SelectionAnalyses/FADE.bf
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<a href="#817efc81f1180519a6136b50a447433f20cf679d">
res/TemplateBatchFiles/SelectionAnalyses/FEL.bf
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<a href="#428ab1297972e0944fd35b5136d40326dd840dcb">
res/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf
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<a href="#af43f80c500c4a3acf886ebcfd048a6a7a3cf361">
res/TemplateBatchFiles/SelectionAnalyses/FitMultiModel.bf
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<li class="file-stats">
<a href="#bc98d7300147ce39ef8ee0f9b35f3252bebd01d2">
res/TemplateBatchFiles/SelectionAnalyses/MEME.bf
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<a href="#80cb7c212661a2afbd05c16dce9f84f45709578e">
res/TemplateBatchFiles/SelectionAnalyses/PRIME.bf
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<a href="#cf5243a3058ebeab74574f8cd2c771cd63a43208">
res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf
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<a href="#13df3044c13d443b9b6ad8712b47d3bc84725272">
res/TemplateBatchFiles/SelectionAnalyses/SLAC.bf
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<li class="file-stats">
<a href="#43faaf1f56e02d91be5b281472029a32276f7b4c">
res/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf
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<li class="file-stats">
<a href="#48abec8e0d198814ad3898dd7c82ef8b52eef776">
res/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf
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<a href="#c259485f7f96dc2ad350d5448508de915c6a9885">
res/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf
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<a href="#c079be28c5231888d711d5c41d1be180223dfce6">
res/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf
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<a href="#5162429bd3f362a69890c6b040d4be37e11a6308">
res/TemplateBatchFiles/files.lst
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<a href="#c50a9ebb34fca832759d3d11698588f8851c99cb">
res/TemplateBatchFiles/libv3/UtilityFunctions.bf
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<a href="#5dfec713e3892a936e8b5a63db56c03bee3ec252">
res/TemplateBatchFiles/libv3/all-terms.bf
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<a href="#94156df91590185798157c724050369c6294262f">
res/TemplateBatchFiles/libv3/models/codon/BS_REL.bf
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<a href="#c7933e171033f4eac9d83419583cca5474f9266c">
res/TemplateBatchFiles/libv3/tasks/estimators.bf
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<a href="#07aceb8d215a75908cea626d9c80bc2a7c06639c">
src/core/global_things.cpp
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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="#d5409d207f9902b4fd1c68a0af284b4294fed610">
src/core/simplelist.cpp
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<li class="file-stats">
<a href="#3db5a40160a9b0d2ceac81e7037e883bdd54b8f7">
src/core/topology.cpp
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<li class="file-stats">
<a href="#aeaccdf9a873c05871ba3cd1bca1ae0e9f8254e4">
src/mains/unix.cpp
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</ul>
<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -307,21 +307,16 @@ endif(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")</td>
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<td class="old_line diff-line-num" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
307
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<td class="new_line diff-line-num" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#-------------------------------------------------------------------------------</span></span>
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<td class="old_line diff-line-num" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>CURL<span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CURL_FOUND</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;">#if(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")</span></span>
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<td class="old_line diff-line-num old" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;"># set(DEFAULT_LIBRARIES " crypto curl ssl")</span></span>
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<td class="old_line diff-line-num old" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;">#else(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")</span></span>
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<td class="old_line diff-line-num old" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;"># set(DEFAULT_LIBRARIES "dl crypto curl ssl")</span></span>
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<td class="old_line diff-line-num old" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;">#endif(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")</span></span>
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<td class="old_line diff-line-num" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">message</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CURL_LIBRARIES</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">st<span class="idiff left">ring</span></span><span class="p">(</span>APPEND DEFAULT_LIBRARIES <span class="s2" style="color: #d14;"><span class="idiff">" "</span></span><span class="idiff right"> </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CURL_LIBRARIES</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;"><span class="idiff left right">li</span>st</span><span class="p">(</span>APPEND DEFAULT_LIBRARIES <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CURL_LIBRARIES</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_definitions</span> <span class="p">(</span>-D__HYPHYCURL__<span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CURL_FOUND</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="cmake"></span>
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<td class="new_line diff-line-num" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>NOT NOZLIB<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>ZLIB 1.2.9<span class="p">)</span></span>
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317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">ZLIB_FOUND</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="cmake"><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">string</span></span><span class="p">(</span>APPEND DEFAULT_LIBRARIES <span class="s2" style="color: #d14;"><span class="idiff">" "</span></span><span class="idiff right"> </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">ZLIB_LIBRARIES</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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324
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="cmake"><span class="idiff left right"> </span><span class="nb" style="color: #0086b3;">include_directories</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">ZLIB_INCLUDE_DIRS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cmake"><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">list</span></span><span class="p">(</span>APPEND DEFAULT_LIBRARIES <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">ZLIB_LIBRARIES</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cmake"><span class="idiff left right"> </span><span class="nb" style="color: #0086b3;">include_directories</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">ZLIB_INCLUDE_DIRS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_definitions</span> <span class="p">(</span>-D__ZLIB__<span class="p">)</span></span>
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326
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">ZLIB_FOUND</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span>NOT NOZLIB<span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -637,6 +632,6 @@ add_test (CONTRAST-FEL HYPHYMP tests/hbltests/libv3/CFEL.wbf)</td>
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637
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>GARD HYPHYMP tests/hbltests/libv3/GARD.wbf<span class="p">)</span></span>
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638
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>FADE HYPHYMP tests/hbltests/libv3/FADE.wbf<span class="p">)</span></span>
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639
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>ABSREL HYPHYMP tests/hbltests/libv3/ABSREL.wbf<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC640" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>FMM HYPHYMP tests/hbltests/libv3/FMM.wbf<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>add_test (FMM HYPHYMP tests/hbltests/libv3/FMM.wbf)</span></span>
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641
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#add_test (NAME ABSREL-MH COMMAND HYPHYMP tests/hbltests/libv3/ABSREL-MH.wbf)</span></span>
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="cmake"></span></pre>
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<li id="0570609ee9b4163f9738e06f4afb1114320867f5">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#0570609ee9b4163f9738e06f4afb1114320867f5"><strong>res/TemplateBatchFiles/AddABias.ibf</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">@@ -47,7 +47,7 @@ function AddABiasREL (ModelMatrixName&, ModelMatrixName2&, biasedBase)</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> t = 1; /* branch length, local parameter */</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> c = 1; /* rate variation */</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> _numericRateMatrix = ModelMatrixName;</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> _numericRateMatrix = <span class="idiff left">Eval ("</span>ModelMatrixName<span class="idiff right">")</span>;</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> /* the probability that site is undergoing biased substitution rates */</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"> global P_bias = 0.1; P_bias :< 0.5;</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">@@ -55,25 +55,29 @@ function AddABiasREL (ModelMatrixName&, ModelMatrixName2&, biasedBase)</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"> category catVar = (2,{{1-P_bias,P_bias}},MEAN,,{{0,1}},0,1);</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> for (ri = 0; ri < 20; ri = ri+1)</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext"> {</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext"> for (ci = ri+1; ci < 20; ci = ci+1)</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"> {</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> for (ri = 0; ri < 20; ri += 1) {</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> // make sure the row is not all 0</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> max_row = Max (_numericRateMatrix[ri][-1], 0);</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> //fprintf (stdout, "\n", ri, ":", max_row, "\t");</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> if (max_row < 1e-10) {</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> for (ci = 0; ci < 20; ci+=1) {</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> _numericRateMatrix[ci][ri] = 1e-6;</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> _numericRateMatrix[ri][ci] = 1e-6;</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> } </span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> }</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> for (ci = ri+1; ci < 20; ci += 1) {</span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext"> ModelMatrixName2[ri][ci] := _numericRateMatrix__[ri__][ci__] * t * c;</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext"> ModelMatrixName2[ci][ri] := _numericRateMatrix__[ri__][ci__] * t * c;</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext"> }</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"> }</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext"> if (biasedBase < 20)</span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext"> {</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> if (biasedBase < 20) {</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext"> global rateBiasTo = 5.0;</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext"> global rateBiasFrom := 1/rateBiasTo;</span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext"> rateBiasTo :>1;</span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext"> relBias :>1; /* UNUSED ?!? */</span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext"> for (ri = 0; ri < 20; ri = ri+1)</span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext"> {</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> for (ri = 0; ri < 20; ri += 1) {</span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext"> if (ri != biasedBase)</span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext"> {</span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext"> ModelMatrixName2[ri][biasedBase] := _numericRateMatrix__[ri__][biasedBase__] * t * c * ((catVar==1)*rateBiasTo+(catVar==0));</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">@@ -81,7 +85,7 @@ function AddABiasREL (ModelMatrixName&, ModelMatrixName2&, biasedBase)</td>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext"> }</span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="plaintext"> }</span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext"> }</span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"> return 1;</span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext">}</span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#1c34e5e2341f7334d9146eb8e633fd86fdc01c3d"><strong>res/TemplateBatchFiles/DirectionalREL.bf</strong></a>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/* define an associative array with key = amino acid and value = integer</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> index for AA in alphabetical order */</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">AAString = "ACDEFGHIKLMNPQRSTVWY";</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">AACharToIdx = {}; /* this is never used :</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">P */</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">for (k=0; k</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">20; k=k</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1)</span></span>
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<pre style="margin: 0;">+<span id="LC8" 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="LC9" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> AACharToIdx </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">AAString</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;"> = k;</span></span>
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<pre style="margin: 0;">+<span id="LC10" 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="LC11" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">SKIP_MODEL_PARAMETER_LIST = 0;</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">#include "AddABias</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="LC15" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">#include "Utility/GrabBag</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bf";</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">test_p_values = {20</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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<pre style="margin: 0;">+<span id="LC18" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC19" 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="LC20" 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="LC21" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> returns stationary distribution vector for amino acids</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> UNUSED?!?</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">function GetEqFreqs (ModelMatrixName&</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> baseFreqs)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">{</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> t = 1;</span></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;"> </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;"> /* duplicate instantaneous rate parameterization from template model */</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> numRateMx = ModelMatrixName;</span></span>
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<pre style="margin: 0;">+<span id="LC30" 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="LC31" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (ri = 0; ri </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 20; ri = ri</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1)</span></span>
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<pre style="margin: 0;">+<span id="LC32" 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="LC33" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (ci = 0; ci </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 20; ci = ci</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1)</span></span>
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<pre style="margin: 0;">+<span id="LC34" 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="LC35" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (ri != ci)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /* multiply entries by base frequencies */</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> numRateMx</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">ri</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">ci</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = numRateMx</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">ri</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">ci</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> * baseFreqs</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">ci</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="LC39" 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="LC40" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /* diagonal entry is sum of off</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">diagonal row entries (Markov process) */</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> numRateMx</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">ri</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">ri</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = numRateMx</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">ri</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">ri</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;"> numRateMx</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">ri</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">ci</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="LC42" 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="LC43" 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="LC44" 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="LC47" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (ri = 0; ri </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 20; ri = ri</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1)</span></span>
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<pre style="margin: 0;">+<span id="LC48" 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="LC49" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> numRateMx </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">ri</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">19</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = 1;</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" 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="LC51" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> numRateMxI = Inverse (numRateMx);</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return numRateMxI </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">19</span><span class="p">][</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC55" 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="LC56" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">SetDialogPrompt ("Protein file to examine:");</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">ChoiceList (reloadFlag</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Reload/New"</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;"> SKIP_NONE</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "New analysis"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"Start a new analysis"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Reload"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"Reload a baseline protein fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Reprocess the results"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"Regenerate sites from model fits</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="LC62" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">ACCEPT_ROOTED_TREES = 1;</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (reloadFlag == 0) {</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /* new analysis</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> fit baseline model */</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /* this should be a protein alignment */</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> DataSet ds = ReadDataFile (PROMPT_FOR_FILE);</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> basePath = LAST_FILE_PATH;</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> DataSetFilter filteredData = CreateFilter (ds</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">1);</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" 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="LC74" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> GetDataInfo (checkCharacters</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> filteredData</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "CHARACTERS");</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (Columns (checkCharacters) != 20)</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "ERROR: please ensure that the input alignment contains protein sequences");</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return 0;</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /* from AddABias</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ibf; select from one of several AA rate matrices estimated from</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> curated alignments (e</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">g</span><span class="nf" style="color: #900; font-weight: 600;">.,</span><span class="c1" style="color: #998; font-style: italic;"> HIV within); by default</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> set rate variation to</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> adaptive 4</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">bin beta</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">gamma </span><span class="nf" style="color: #900; font-weight: 600;">--</span><span class="c1" style="color: #998; font-style: italic;"> argument 0 skips dialog to set </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">pickATarget</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="LC84" 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="LC85" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> promptModel (0);</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ExecuteAFile (HYPHY_LIB_DIRECTORY </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "TemplateBatchFiles" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> DIRECTORY_SEPARATOR </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "queryTree</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bf");</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ChoiceList (fixFB</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Fix Branch"</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;"> SKIP_NONE</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Unknown root"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"The character at the root of the tree is drawn from the stationary distribution"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Fix 1st sequence as root"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"The 1st sequence in the file (assumed to be a direct descendant of the root) is used to populate the root sequences</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="LC91" 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="LC92" 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="LC93" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /* check if the tree is rooted */</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" 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="LC95" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> treeAVL = givenTree^0;</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rootNode = treeAVL</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">(treeAVL</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"Root"</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (Abs(rootNode</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"Children"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) != 2) {</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "ERROR: please ensure that the tree is rooted");</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return 0;</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> root_left = "givenTree</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;"> (treeAVL</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">(rootNode</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"Children"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"Name"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </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;">t";</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> root_right = "givenTree</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;"> (treeAVL</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">(rootNode</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"Children"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"Name"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </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;">t";</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (fixFB</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;">0) {</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /* branch to first sequence is collapsed to length zero;</span></span>
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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;"> enforcing identifiability with root sequence */</span></span>
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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;"> ExecuteCommands ("givenTree</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;">TipName(givenTree</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0)</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">t:=0");</span></span>
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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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109
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<pre style="margin: 0;">+<span id="LC109" 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="LC110" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (fixFB </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 0)</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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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;"> return 0;</span></span>
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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;"> }</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /* only the sum of branch lengths leading to two immediate descendants</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> of root can be estimated; this measure prevents one of the branches</span></span>
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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;"> from collapsing to zero length */</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ExecuteCommands (root_left </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;"> root_right); </span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> LikelihoodFunction lf = (filteredData</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> givenTree);</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">PHASE 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> Standard model fit\n"); </span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> VERBOSITY_LEVEL = 1;</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> AUTO_PARALLELIZE_OPTIMIZE = 1;</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Optimize (res0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">lf);</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> AUTO_PARALLELIZE_OPTIMIZE = 0;</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> VERBOSITY_LEVEL = </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1;</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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132
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /* export baseline model LF */</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> LIKELIHOOD_FUNCTION_OUTPUT = 7;</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> outPath = basePath </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;">base";</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (outPath</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> CLEAR_FILE</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> lf);</span></span>
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137
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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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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> baselineLogL = res0</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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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">else {</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /* import baseline LF from file */</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> modelNameString = "_customAAModelMatrix";</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> SetDialogPrompt ("Locate an existing fit:");</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ExecuteAFile (PROMPT_FOR_FILE);</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" 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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<td class="new_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if ((lfInfo</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"Models"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> == "mtREVModel")</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> modelNameString = "mtREVMatrix"; </span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> bpSplit = splitFilePath (LAST_FILE_PATH);</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> basePath = bpSplit</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"DIRECTORY"</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;"> bpSplit</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"FILENAME"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> outPath = basePath </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;">base";</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> treeString = Format (givenTree</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0); /* topology only</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> no branch lengths */</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="brainfuck"></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> treeAVL = givenTree^0;</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rootNode = treeAVL</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">(treeAVL</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"Root"</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (Abs(rootNode</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"Children"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) != 2)</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "ERROR: please ensure that the tree is rooted");</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return 0;</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="brainfuck"></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="brainfuck"></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ChoiceList (fixFB</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Fix Branch"</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;"> SKIP_NONE</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Unknown root"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"The character at the root of the tree is drawn from the stationary distribution"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Fix 1st sequence as root"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"The 1st sequence in the file (assumed to be a direct descendant of the root) is used to populate the root sequences</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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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;"> if (fixFB</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;">0)</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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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;"> ExecuteCommands ("givenTree</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;">TipName(givenTree</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0)</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">t:=0");</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> else</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (fixFB </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 0)</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return 0;</span></span>
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> LFCompute (lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">LF_START_COMPUTE);</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> LFCompute (lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">baselineLogL);</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> LFCompute (lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">LF_DONE_COMPUTE);</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="brainfuck"></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="brainfuck"></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/* when the heck does biasedTree get called? It's tucked inside runAFit() in AddABias</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ibf</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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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">root_left = "biasedTree</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;"> (treeAVL</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">(rootNode</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"Children"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"Name"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </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;">t";</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">root_right = "biasedTree</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;"> (treeAVL</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">(rootNode</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"Children"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"Name"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </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;">t";</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="brainfuck"></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="brainfuck"></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/* vector of branch lengths for entire tree */</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">baselineBL = BranchLength (givenTree</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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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="brainfuck"></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">referenceL = (baselineBL * (Transpose(baselineBL)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"1"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">))</span><span 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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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="brainfuck"></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">summaryPath = basePath</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;">summary";</span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">substitutionsPath = basePath</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">"_subs</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">csv";</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">siteReportMap = basePath</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">"_bysite</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">csv";</span></span>
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<td class="new_line diff-line-num new" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fprintf (summaryPath</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> CLEAR_FILE</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> KEEP_OPEN);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fprintf (stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">PHASE 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="p">]</span><span class="c1" style="color: #998; font-style: italic;"> Standard model fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> Log</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">L = "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">baselineLogL</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;"> Tree length = "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">referenceL</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> " subs/site \n"); </span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fprintf (summaryPath</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;">PHASE 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="p">]</span><span class="c1" style="color: #998; font-style: italic;"> Standard model fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> Log</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">L = "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">baselineLogL</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;"> Tree length = "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">referenceL</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> " subs/site \n"); </span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="brainfuck"></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="brainfuck"></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">ExecuteAFile (HYPHY_LIB_DIRECTORY </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "TemplateBatchFiles" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> DIRECTORY_SEPARATOR </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "Utility" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> DIRECTORY_SEPARATOR </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "GrabBag</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bf");</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">ExecuteAFile (HYPHY_LIB_DIRECTORY </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "TemplateBatchFiles" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> DIRECTORY_SEPARATOR </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "Utility" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> DIRECTORY_SEPARATOR </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "AncestralMapper</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bf");</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="brainfuck"></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fixGlobalParameters ("lf");</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="brainfuck"></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">byResidueSummary = {};</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">bySiteSummary = {};</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="brainfuck"></span>
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211
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<pre style="margin: 0;">+<span id="LC211" 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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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="brainfuck"></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (MPI_NODE_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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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">{</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> MPINodeStatus = {MPI_NODE_COUNT</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">1}</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">for (residue = 0; residue </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 20; residue = residue </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 1)</span></span>
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<pre style="margin: 0;">+<span id="LC221" 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="LC222" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (reloadFlag == 2) /* regenerate sites from results files */</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> lfb_MLES = {2</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">1};</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ExecuteAFile (basePath </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> AAString</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">residue</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="LC226" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> LFCompute (lfb</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">LF_START_COMPUTE);</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> LFCompute (lfb</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">res);</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> LFCompute (lfb</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">LF_DONE_COMPUTE); </span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> lfb_MLES </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;"> = res;</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> DoResults (residue);</span></span>
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<pre style="margin: 0;">+<span id="LC231" 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="LC232" 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="LC233" 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="LC234" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> AddABiasREL (modelNameString</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"biasedMatrix"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">residue); /* returns biasedMatrix object */</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> global P_bias2 := 1;</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> global relBias := 1;</span></span>
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<pre style="margin: 0;">+<span id="LC237" 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="LC238" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /* vectorOfFrequencies comes from Custom_AA_empirical</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mdl</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> in turn imported from a file such as "HIVWithin" */</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /* rate matrix is multiplied by this vector (third argument) */</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Model biasedModel = (biasedMatrix</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> vectorOfFrequencies</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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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Tree biasedTree = treeString;</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> global treeScaler = 1;</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /* constrains tree to be congruent to that estimated under baseline model */</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ReplicateConstraint ("this1</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;">?:=treeScaler*this2</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">?</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">?__"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">biasedTree</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">givenTree);</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ExecuteCommands (root_left </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;"> root_left);</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ExecuteCommands (root_right </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;"> root_right);</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> LikelihoodFunction lfb = (filteredData</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> biasedTree);</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (MPI_NODE_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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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> SendAJob (residue);</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> else</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Optimize (lfb_MLES</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">lfb);</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> DoResults (residue);</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="brainfuck"></span>
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263
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<pre style="margin: 0;">+<span id="LC263" 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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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="brainfuck"></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (MPI_NODE_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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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">{</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> jobsLeft = ({1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">MPI_NODE_COUNT</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1}</span><span class="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;"> * MPINodeStatus</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"_MATRIX_ELEMENT_VALUE_</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;">=0"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="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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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="brainfuck"></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (nodeID = 0; nodeID </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> jobsLeft; nodeID = nodeID </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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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> MPIReceive (</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;"> fromNode</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> theJob);</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> oldRes = MPINodeStatus</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fromNode</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ExecuteCommands (theJob);</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> DoResults (oldRes); </span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="brainfuck"></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/*</span><span class="nf" style="color: #900; font-weight: 600;">------------------------------------------------------------------------------</span><span class="c1" style="color: #998; font-style: italic;">*/</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="brainfuck"></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fprintf (substitutionsPath</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> CLEAR_FILE</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> KEEP_OPEN</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;">From</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">To</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">Count");</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fprintf (siteReportMap</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> CLEAR_FILE</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> KEEP_OPEN</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Site");</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">for (k=0; k</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">20; k=k</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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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">{</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (siteReportMap</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> AAString</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fprintf (siteReportMap</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\nLRT 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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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="brainfuck"></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">test_p_values = test_p_values % 0;</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">rejectedHypotheses = {};</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="brainfuck"></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">for (k=0; k</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">20; k=k</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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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">{</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> pv = (byResidueSummary</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">AAString</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"p"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (siteReportMap</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> pv);</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="brainfuck"></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fprintf (stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\nResidues (and p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">values) for which there is evidence of directional selection\n");</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fprintf (summaryPath</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\nResidues (and p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">values) for which there is evidence of directional selection");</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="brainfuck"></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">for (k=0; k</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">20; k=k</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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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">{</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (test_p_values</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> (0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">05/(20</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">k)))</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rejectedHypotheses </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">test_p_values</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;"> = 1;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="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="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rejectedHypotheses </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">AAString</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">test_p_values</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]]]</span><span class="c1" style="color: #998; font-style: italic;"> = 1;</span></span>
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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;"> fprintf (stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\n\t"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> AAString</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">test_p_values</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">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;"> " : "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">test_p_values</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> );</span></span>
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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;"> fprintf (summaryPath</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\n\t"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> AAString</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">test_p_values</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">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;"> " : "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">test_p_values</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> );</span></span>
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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;"> else</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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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;"> break;</span></span>
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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;"> }</span></span>
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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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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="brainfuck"></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fprintf (stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\n");</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fprintf (summaryPath</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\n");</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="brainfuck"></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="brainfuck"></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">ancCacheID = _buildAncestralCache ("lf"</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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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">outputcount = 0;</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">for (k=0; k</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">filteredData</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sites; k=k</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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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">{</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> thisSite = _substitutionsBySite (ancCacheID</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">k);</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" 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="LC326" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (char1 = 0; char1 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 20; char1 = char1</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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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (char2 = 0; char2 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 20; char2 = char2</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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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (char1 != char2 && (thisSite</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"COUNTS"</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;">char1</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">char2</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> { </span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ccount = (thisSite</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"COUNTS"</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;">char1</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">char2</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (substitutionsPath</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;"> k</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> AAString</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">char1</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> AAString</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">char2</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ccount);</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (Abs(bySiteSummary</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">))</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (siteReportMap</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;"> k</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1);</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> didSomething = 0;</span></span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> pv = 0;</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (k2=0; k2</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">20; k2=k2</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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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (Abs((byResidueSummary</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">AAString</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k2</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;">"BFs"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) == 0 || rejectedHypotheses</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k2</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> == 0)</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (siteReportMap</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;">N/A");</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> else</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" 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="LC353" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> thisSitePV = ((byResidueSummary</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">AAString</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k2</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;">"BFs"</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;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> pv = Max(pv</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">thisSitePV);</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (siteReportMap</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> thisSitePV); </span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (pv </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;"> 100)</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> didSomething = 1;</span></span>
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<pre style="margin: 0;">+<span id="LC359" 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="LC360" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (!didSomething)</span></span>
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<pre style="margin: 0;">+<span id="LC364" 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="LC365" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> continue;</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (outputcount == 0)</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> outputcount = 1;</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\nThe list of sites which show evidence of directional selection (Bayes Factor </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;"> 20)\n"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "together with the target residues and inferred substitution counts\n");</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (summaryPath</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\nThe list of sites which show evidence of directional selection (Bayes Factor </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;"> 20)\n"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "together with the target residues and inferred substitution counts\n");</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } </span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\nSite "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Format (k</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;">8</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;"> " (max BF = "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> pv</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ")\n Preferred residues: ");</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (summaryPath</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\nSite "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Format (k</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;">8</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;"> " (max BF = "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> pv</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ")\n Preferred residues: ");</span></span>
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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;"> </span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (k2 = 0; k2 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> Abs (bySiteSummary</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">); k2=k2</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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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> thisChar = (bySiteSummary</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k2</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (rejectedHypotheses</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">thisChar</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> thisChar);</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (summaryPath</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> thisChar);</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="brainfuck"></span>
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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;"> fprintf (stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\n Substitution counts:");</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (summaryPath</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\n Substitution counts:");</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="brainfuck"></span>
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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;"> for (char1 = 0; char1 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 20; char1 = char1</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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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (char2 = char1</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1; char2 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 20; char2 = char2</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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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ccount = (thisSite</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"COUNTS"</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;">char1</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">char2</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ccount2 = (thisSite</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"COUNTS"</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;">char2</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">char1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (ccount</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">ccount2)</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> { </span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\n\t"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> AAString</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">char1</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="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;"> AAString</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">char2</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ":"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Format (ccount</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 5</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "/"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> AAString</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">char2</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="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;"> AAString</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">char1</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ":"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Format (ccount2</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 5</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0));</span></span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (summaryPath</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\n\t"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> AAString</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">char1</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="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;"> AAString</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">char2</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ":"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Format (ccount</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 5</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "/"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> AAString</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">char2</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="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;"> AAString</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">char1</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ":"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Format (ccount2</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 5</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0));</span></span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC407" 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="LC408" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">} </span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="brainfuck"></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">_destroyAncestralCache (ancCacheID);</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fprintf (substitutionsPath</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> CLOSE_FILE);</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fprintf (summaryPath</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> CLOSE_FILE);</span></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fprintf (siteReportMap</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> CLOSE_FILE);</span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fprintf (stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\n");</span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/*</span><span 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="LC419" 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="LC420" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Compute the difference vector between the stationary distribution at the root (efv) and the expected</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> distribution of residues after time t0</span><span class="nf" style="color: #900; font-weight: 600;">.</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">function computeDelta (ModelMatrixName&</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> efv</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> t_0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> which_cat)</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">{</span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> t = t_0;</span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> c = 1;</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> catVar = which_cat;</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rmx = ModelMatrixName;</span></span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (r=0; r</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">20; r=r</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1)</span></span>
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<pre style="margin: 0;">+<span id="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;"> diag = 0;</span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (c=0; c</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">20; c=c</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1)</span></span>
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<pre style="margin: 0;">+<span id="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;"> rmx</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">r</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;"> = rmx</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">r</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;"> * efv</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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<pre style="margin: 0;">+<span id="LC435" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> diag = diag </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> rmx</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">r</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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<pre style="margin: 0;">+<span id="LC436" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rmx</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">r</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">r</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = diag;</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return Transpose(efv)*(Exp (rmx) </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> {20</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">20}</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"_MATRIX_ELEMENT_ROW_==_MATRIX_ELEMENT_COLUMN_"</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="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="LC442" 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="LC443" class="line" lang="brainfuck"></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;">function SendAJob (residueIn)</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></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;"> for (nodeID = 0; nodeID </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> MPI_NODE_COUNT </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1; nodeID = nodeID </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 1)</span></span>
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<pre style="margin: 0;">+<span id="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="LC448" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (MPINodeStatus</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">nodeID</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 0) /* semaphore indicates available node */</span></span>
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449
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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></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;"> MPINodeStatus</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">nodeID</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = residueIn;</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;"> MPISend (nodeID</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;">lfb);</span></span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> break;</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;"> }</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;"> if (nodeID == MPI_NODE_COUNT </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> 1) /* looped through semaphore with no idle nodes */</span></span>
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456
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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;"> MPIReceive (</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;"> fromNode</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> theJob); /* wait until one of the node completes its job */</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;"> oldRes = MPINodeStatus</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fromNode</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> MPISend (fromNode</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">lfb);</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;"> MPINodeStatus</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fromNode</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = residueIn;</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;"> ExecuteCommands (theJob); /* load serialized LF into master node memory */</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;"> DoResults (oldRes);</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;"> }</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;"> return 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;">}</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 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="LC469" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">function DoResults (residueIn)</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;">{</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> residueC = AAString</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">residueIn</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="LC472" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">PHASE "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">residueIn</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> Model biased for "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">residueC</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"\n"); </span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (summaryPath</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;">PHASE "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">residueIn</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> Model biased for "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">residueC</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"\n"); </span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="brainfuck"></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;"> pv = 1</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">CChi2(2(lfb_MLES</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">baselineLogL)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3); /* approximate 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="LC476" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">PHASE "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">residueIn</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">2</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> Finished with the model biased for "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">residueC</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;"> Log</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">L = "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">Format(lfb_MLES</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">8</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;">"\n"); </span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (summaryPath</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;">PHASE "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">residueIn</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">2</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> Finished with the model biased for "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">residueC</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;"> Log</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">L = "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">Format(lfb_MLES</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">8</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;">"\n"); </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;"> </span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fr1 = P_bias;</span></span>
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<pre style="margin: 0;">+<span id="LC480" 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="LC481" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rateAccel1 = (computeDelta("biasedMatrix"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">vectorOfFrequencies</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">referenceL</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">1))</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">residueIn</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="LC482" 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="LC483" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\n\tBias term = "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Format(rateBiasTo</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">8</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "\n\tproportion = "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Format(fr1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">8</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "\n\tExp freq increase = "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Format(rateAccel1*100</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">8</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "%"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "\n\tp</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;"> Format(pv</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">8</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"\n");</span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (summaryPath</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\n\tBias term = "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Format(rateBiasTo</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">8</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "\n\tproportion = "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Format(fr1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">8</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "\n\tExp freq increase = "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Format(rateAccel1*100</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">8</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "%"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "\n\tp</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;"> Format(pv</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">8</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"\n");</span></span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (reloadFlag != 2)</span></span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> LIKELIHOOD_FUNCTION_OUTPUT = 7;</span></span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> outPath = basePath </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> residueC;</span></span>
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (outPath</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> CLEAR_FILE</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> lfb);</span></span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> byResidueSummary </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">residueC</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = {};</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (byResidueSummary </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">residueC</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;">"p"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = pv; </span></span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="brainfuck"></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> test_p_values </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">residueIn</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;"> = pv;</span></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> test_p_values </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">residueIn</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;"> = residueIn;</span></span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="brainfuck"></span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /*if (pv </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">0025)*/</span></span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (byResidueSummary </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">residueC</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;">"sites"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = {}; </span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (byResidueSummary </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">residueC</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;">"BFs"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = {}; </span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ConstructCategoryMatrix (mmx</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">lfb</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">COMPLETE);</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> GetInformation (catOrder</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> lfb); </span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> dim = Columns (mmx);</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _MARGINAL_MATRIX_ = {2</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> dim};</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" 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="LC515" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> GetInformation (cInfo</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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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> GetInformation (_CATEGORY_VARIABLE_CDF_</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> catVar);</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ccc = Columns (cInfo);</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _CATEGORY_VARIABLE_CDF_ = _CATEGORY_VARIABLE_CDF_</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;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (catOrder </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;"> == "c")</span></span>
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<pre style="margin: 0;">+<span id="LC522" 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="LC523" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (k=0; k</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">dim; k=k</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1)</span></span>
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<pre style="margin: 0;">+<span id="LC524" 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="LC525" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (k2 = 0; k2 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> ccc; k2=k2</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1)</span></span>
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<pre style="margin: 0;">+<span id="LC526" 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="LC527" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _MARGINAL_MATRIX_ </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;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _MARGINAL_MATRIX_ </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;">k</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;"> mmx</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">2*k2</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> *cInfo</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;">k2</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="LC528" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _MARGINAL_MATRIX_ </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;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _MARGINAL_MATRIX_ </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;">k</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;"> mmx</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">2*k2</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">*cInfo</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;">k2</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="LC529" 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="LC530" 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="LC531" 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="LC532" 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="LC533" 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="LC534" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (k=0; k</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">dim; k=k</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1)</span></span>
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<pre style="margin: 0;">+<span id="LC535" 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="LC536" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (k2 = 0; k2 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> ccc; k2=k2</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1)</span></span>
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<pre style="margin: 0;">+<span id="LC537" 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="LC538" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _MARGINAL_MATRIX_ </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;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _MARGINAL_MATRIX_ </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;">k</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;"> mmx</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k2</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">*cInfo</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;">k2</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="LC539" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _MARGINAL_MATRIX_ </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;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _MARGINAL_MATRIX_ </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;">k</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;"> mmx</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">ccc</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">k2</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">*cInfo</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;">k2</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="LC540" 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="LC541" 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="LC542" 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="LC544" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _sites = Columns (_MARGINAL_MATRIX_);</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _classes = Rows (_MARGINAL_MATRIX_);</span></span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _siteVector = {1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _classes};</span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> STASH_MARGINAL_MATRIX = _MARGINAL_MATRIX_;</span></span>
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _post :</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 1e300;</span></span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _norm :</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 1e300;</span></span>
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (_counter = 0; _counter </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> _sites; _counter = _counter </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 1) {</span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _norm = 0;</span></span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (_counter2 = 0; _counter2 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> _classes; _counter2 = _counter2 </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 1)</span></span>
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<pre style="margin: 0;">+<span id="LC557" 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="LC558" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _post = _MARGINAL_MATRIX_</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_counter2</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">_counter</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> * _CATEGORY_VARIABLE_CDF_ </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;">_counter2</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _norm = _norm </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> _post;</span></span>
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _siteVector </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_counter2</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _post;</span></span>
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _siteVector = _siteVector * (1/_norm);</span></span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (_counter2 = 0; _counter2 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> _classes; _counter2 = _counter2 </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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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _MARGINAL_MATRIX_</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_counter2</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">_counter</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _siteVector </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_counter2</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="brainfuck"></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> prior = (_CATEGORY_VARIABLE_CDF_</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)/(1</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">_CATEGORY_VARIABLE_CDF_</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" 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="LC573" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (k=0; k</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">dim; k=k</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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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> bayesF = _MARGINAL_MATRIX_</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;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">/_MARGINAL_MATRIX_</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;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">/prior;</span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ((byResidueSummary </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">residueC</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;">"BFs"</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;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = bayesF;</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (bayesF </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;"> 100)</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ((byResidueSummary </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">residueC</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;">"sites"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">Abs((byResidueSummary </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">residueC</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;">"sites"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = k</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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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (Abs(bySiteSummary</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) == 0)</span></span>
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<pre style="margin: 0;">+<span id="LC581" 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="LC582" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> bySiteSummary</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = {};</span></span>
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583
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<pre style="margin: 0;">+<span id="LC583" 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="LC584" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (bySiteSummary</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">Abs(bySiteSummary</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = residueC;</span></span>
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585
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<pre style="margin: 0;">+<span id="LC585" 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="LC586" 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="LC587" 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="LC588" 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="LC589" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return 0;</span></span>
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#595b42362bc80e51259da598ac8ff2dd32cd7358"><strong>res/TemplateBatchFiles/GARD.bf</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -248,6 +248,7 @@ for (_pattern_; in; alignments.Extract_site_patterns ("gard.filter")) {</td>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">variableSiteMap = Transpose (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">DictToArray (gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">variableSiteMap)) % 0; // sort by 1st column</span></span>
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250
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">variableSites = Rows (gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">variableSiteMap);</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">inverseVariableSiteMap = {};</span></span>
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252
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253
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">for (index</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> pattern; in; gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">variableSiteMap) {</span></span>
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253
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254
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">inverseVariableSiteMap</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">pattern</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = index;</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#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">@@ -671,6 +671,10 @@ console.log ( "Likelihood ratio test for episodic diversifying positive selectio</td>
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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;">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;">stopTimer (busted</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">timers</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Overall");</span></span>
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<pre style="margin: 0;"> <span id="LC673" class="line" lang="brainfuck"></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;">GetString (_hpv</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">HYPHY_VERSION</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="LC675" 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;">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;">runtime</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _hpv;</span></span>
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="brainfuck"></span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="brainfuck"></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;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SpoolJSON (busted</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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679
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<pre style="margin: 0;"> <span id="LC679" class="line" lang="brainfuck"></span>
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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;">return busted</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json;</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#f029f7293cd2f0d6999ed6bdfd41727a79f56162"><strong>res/TemplateBatchFiles/SelectionAnalyses/FADE.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">@@ -811,6 +811,9 @@ utility.ForEachPair (fade.sites_found_summary, "_residue_", "_count_",</td>
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<pre style="margin: 0;"> <span id="LC811" class="line" lang="brainfuck"></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;">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;">stopTimer (fade</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;"> "Overall");</span></span>
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813
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<pre style="margin: 0;"> <span id="LC813" class="line" lang="brainfuck"></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;">GetString (_hpv</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">HYPHY_VERSION</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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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;">fade</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;">runtime</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _hpv;</span></span>
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816
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="brainfuck"></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;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SpoolJSON (fade</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;"> fade</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alignment_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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818
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<pre style="margin: 0;"> <span id="LC818" class="line" lang="brainfuck"></span>
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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;">// HELPER FUNCTIONS GO HERE</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">@@ -93,25 +93,12 @@ KeywordArgument ("tree", "A phylogenetic tree (optionally annotated with {})", n</td>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">KeywordArgument ("branches"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Branches to test"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "All");</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">KeywordArgument ("srv"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Include synonymous rate variation in the model"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Yes");</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">KeywordArgument ("pvalue"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "The p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">value threshold to use when testing for selection"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">1");</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">KeywordArgument ("ci"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Compute profile likelihood confidence intervals for each variable site"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "No");</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">// One additional KeywordArgument ("output") is called below after namespace fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers = {{"alpha"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Synonymous substitution rate at a site"}</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"beta"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Non</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">synonymous substitution rate at a site"}</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"alpha=beta"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "The rate estimate under the neutral model"}</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"LRT"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Likelihood ration test statistic for beta = alpha</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> versus beta &neq; alpha"}</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"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;"> "Asymptotic p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">value for evidence of selection</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;">e</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> beta &neq; alpha"}</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"Total branch length"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "The total length of branches contributing to inference at this site</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> and used to scale dN</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">dS"}};</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">This table is meant for HTML rendering in the results web</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">app; can use HTML characters</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> the second column</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">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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<pre style="margin: 0;">-<span id="LC110" 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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<pre style="margin: 0;">-<span id="LC111" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC113" 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;">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;"> "LRT"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Selection detected?"}};</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fel</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;"> 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: 16</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">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>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">namespace fel {</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> LoadFunctionLibrary ("modules/shared</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">load</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">file</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bf");</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -130,9 +117,48 @@ if (fel.srv == "Yes"){</td>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/* Prompt for p value threshold */</span></span>
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<pre style="margin: 0;"> <span id="LC118" 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;">pvalue = io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">PromptUser ("\n</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;">Select the p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">value threshold to use when testing for selection"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">1</span><span 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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<pre style="margin: 0;"> <span id="LC119" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC120" 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;">ci = "Yes" == io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SelectAnOption( {</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"Yes"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Compute profile likelihood confidence intervals for dN/dS at each site (~2x slower)</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">"}</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"No"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">Default</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> Do not compute likelihood confidence intervals"}}</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;"> "Compute profile likelihood intervals for site</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">level dN/dS");</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="brainfuck"></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;">KeywordArgument ("resample"</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;">Advanced setting</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> will result in MUCH SLOWER run time</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> Perform parametric bootstrap resampling to derive site</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">level null LRT distributions up to this many replicates per site</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> Recommended use for small to medium (</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">30 sequences) datasets"</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="LC126" 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;">resample = io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">PromptUser ("\n</span><span class="nb" style="color: #0086b3;">></span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">Advanced setting</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> will result in MUCH SLOWER run time</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> Perform parametric bootstrap resampling to derive site</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">level null LRT distributions up to this many replicates per site</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> Recommended use for small to medium (</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">30 sequences) datasets"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">50</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 class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">TRUE);</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">KeywordArgument ("output"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Write the resulting JSON to this file (default is to save to the same path as the alignment file </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 'FEL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json')"</span><span class="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;">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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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<pre style="margin: 0;"> <span id="LC129" 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;">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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">PromptUserForFilePath ("Save the resulting JSON file to");</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ci") {</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers = {</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="brainfuck"><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;"> "Synonymous substitution rate at a site"}</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"beta"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Non</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">synonymous substitution rate at a site"}</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"alpha=beta"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "The rate estimate under the neutral model"}</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"LRT"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Likelihood ration test statistic for beta = alpha</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> versus beta &neq; alpha"}</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="brainfuck"><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;"> "Asymptotic p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">value for evidence of selection</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;">e</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> beta &neq; alpha"}</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;"> {"Total branch length"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "The total length of branches contributing to inference at this site</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> and used to scale dN</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">dS"}</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"dN/dS LB"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "95% profile likelihood CI lower bound for dN/dS (if available)"}</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"dN/dS MLE"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Point estimate for site dN/dS"}</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;"> {"dN/dS UB"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "95% profile likelihood CI upper bound for dN/dS (if available)"}</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;"> };</span></span>
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<pre style="margin: 0;">+<span id="LC144" 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;">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;"> "LRT"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Selection detected?"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"dN/dS with confidence intervals"}};</span></span>
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<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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<pre style="margin: 0;">+<span id="LC145" 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;">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;"> 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: 16</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">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>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">} else {</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" 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;">table_headers = {{"alpha"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Synonymous substitution rate at a site"}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"beta"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Non</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">synonymous substitution rate at a site"}</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"alpha=beta"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "The rate estimate under the neutral model"}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"LRT"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Likelihood ration test statistic for beta = alpha</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> versus beta &neq; alpha"}</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="brainfuck"><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;"> "Asymptotic p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">value for evidence of selection</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;">e</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> beta &neq; alpha"}</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"Total branch length"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "The total length of branches contributing to inference at this site</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> and used to scale dN</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">dS"}};</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" 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;">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;"> "LRT"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Selection detected?"}};</span></span>
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<td class="new_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
155
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<pre style="margin: 0;">+<span id="LC155" 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;">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;"> 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: 16</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">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>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="brainfuck"></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="brainfuck"></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="brainfuck"></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="brainfuck"></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="brainfuck"></span>
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_count = Abs (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">filter_specification);</span></span>
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<pre style="margin: 0;"> <span id="LC163" 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('FEL'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 'selector'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 'Branches to include in the FEL analysis');</span></span>
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<pre style="margin: 0;"> <span id="LC164" 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">@@ -304,16 +330,14 @@ model.generic.AddGlobal (fel.site.mg_rev, "fel.beta_scaler_nuisance", fel.site_b</td>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">DeclareGlobal (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scalers</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="LC331" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC333" 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="LC309" 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>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC334" 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;"> sim_mode) {</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC336" 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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<pre style="margin: 0;">-<span id="LC314" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ExecuteCommands (filter_data);</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ExecuteCommands (filter_data);<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> __make_filter ((lfInfo</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"Datafilters"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetEnvVariable ("USE_LAST_RESULTS"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> TRUE);</span></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">srv"){</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -382,7 +406,6 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod</td>
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382
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<pre style="margin: 0;"> <span id="LC406" 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;">beta_scaler_test" = 1;</span></span>
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta_scaler_nuisance" = 1;</span></span>
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408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetEnvVariable ("VERBOSITY_LEVEL"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 10);</span></span>
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<pre style="margin: 0;"> <span id="LC409" 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="LC410" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Optimize (results</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -393,30 +416,71 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod</td>
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<pre style="margin: 0;"> <span id="LC416" 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="LC417" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> );</span></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //assert (0);</span></span>
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //Optimize (results</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf);</span></span>
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //alternative = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ExtractMLEs (lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping);</span></span>
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<pre style="margin: 0;">-<span id="LC400" 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</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">globals_only" : TRUE});</span></span>
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<pre style="margin: 0;">-<span id="LC401" 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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<pre style="margin: 0;">+<span id="LC419" 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="LC420" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ci = None;</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ci") {</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">srv") {</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> lf_stash = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">TakeLFStateSnapshot (lf);</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> global omega_ratio_for_ci;</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" 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;">alpha_scaler" == 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">0) { // has no syn_variation</span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha_scaler" = 1e</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">8;</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" 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="LC428" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> omega_ratio_for_ci :</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 10000;</span></span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> omega_ratio_for_ci :</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;">0;</span></span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> omega_ratio_for_ci = ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta_scaler_test" / ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha_scaler";</span></span>
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431
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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 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_scaler_test" := omega_ratio_for_ci * ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha_scaler";</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;"> ci = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetProfileCI (&omega_ratio_for_ci</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">95);</span></span>
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<pre style="margin: 0;">+<span id="LC434" 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</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> lf_stash);</span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ci = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetProfileCI ("fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta_scaler_test"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">95);</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </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;"> if (sim_mode) {</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;"> lrt = 2*results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">; </span></span>
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<pre style="margin: 0;">+<span id="LC442" 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="LC443" 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</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">globals_only" : TRUE});</span></span>
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<pre style="margin: 0;">+<span id="LC444" 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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<pre style="margin: 0;">+<span id="LC445" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="brainfuck"></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;"> ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha_scaler" = (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha_scaler" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 3*^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta_scaler_test")/4;</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;"> 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;">beta_scaler_test"</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_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="LC449" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //Optimize (results</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {"OPTIMIZATION_METHOD" : "nedler</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">mead"});</span></span>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Optimize (results</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf);</span></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //Null = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ExtractMLEs (lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping);</span></span>
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Null = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ExtractMLEsOptions (lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">globals_only" : TRUE});</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (sim_mode) {</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;"> return lrt </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> 2*results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">+<span id="LC454" 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="LC455" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Null = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ExtractMLEsOptions (lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">globals_only" : TRUE});</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Null </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log_likelihood")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">+<span id="LC457" 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>
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Null </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log_likelihood")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">+<span id="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;"> if (!sim_mode) {</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;"> if (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">resample") {</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;"> N = ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">resample";</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;"> sims = {};</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;"> GetDataInfo (fi</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^((lfInfo</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"Datafilters"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "PARAMETERS");</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;"> //Export (lfe</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf);</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //console</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log (lfe);</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (i = 0; i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> N; i</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">=1) { </span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> DataSet null_sim = SimulateDataSet (^lf);</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> DataSetFilter null_filter = CreateFilter (null_sim</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;">fi</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"EXCLUSIONS"</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="LC470" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sims </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">serialize_site_filter (&null_filter</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="LC471" 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="LC472" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> null_LRT = {N</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">1};</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (i = 0; i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> N; i</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">=1) { </span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> is = 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;"> sims</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 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;"> TRUE);</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;"> null_LRT</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;"> = is;</span></span>
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<pre style="margin: 0;">+<span id="LC476" 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="LC477" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return {utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">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 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 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;">simulated"): null_LRT};</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;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC479" 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="LC480" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /*</span></span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Export (lfs</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf);</span></span>
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (MESSAGE_LOG</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> lfs);</span></span>
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> assert (0);</span></span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return {utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">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 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>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return {utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">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 class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">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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<pre style="margin: 0;">+<span id="LC483" 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;">confidence_interval"): ci};</span></span>
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<pre style="margin: 0;"> <span id="LC484" 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="LC485" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/* echo to screen calls */</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">@@ -424,20 +488,38 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod</td>
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<pre style="margin: 0;"> <span id="LC488" 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;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">counts = {{0</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="LC489" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC491" 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;">ci") {</span></span>
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<pre style="margin: 0;">+<span id="LC492" 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;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">positive_site = {{"" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (1</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">((fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">filter_specification</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">partition</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">coverage</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">site</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC493" 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;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 1</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">10</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>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(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;">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;">10</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>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">3</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">10</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Pos</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;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">4</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">6</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">4)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">7</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;"> "(" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">6</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">7</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 class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">8</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;">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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<pre style="margin: 0;"> <span id="LC499" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC428" 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;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">positive_site = {{"" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (1</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">((fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">filter_specification</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">partition</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">coverage</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">site</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC429" 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;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 1</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">10</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>
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(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;">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;">10</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>
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">3</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">10</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3)</span><span class="nf" style="color: #900; font-weight: 600;">,</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;"> "Pos</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;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">4</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">6</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">4)}};</span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 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;">negative_site = {{"" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (1</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">((fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">filter_specification</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">partition</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">coverage</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">site</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC501" 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;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 1</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">10</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>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(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;">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;">10</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>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">3</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">10</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Neg</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;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">4</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">6</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">4)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">7</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;"> "(" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">6</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">7</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 class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">8</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;">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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<pre style="margin: 0;"> <span id="LC507" class="line" lang="brainfuck"></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;">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;">negative_site = {{"" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (1</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">((fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">filter_specification</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">partition</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">coverage</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">site</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC436" 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;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 1</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">10</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>
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(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;">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;">10</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>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">3</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">10</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3)</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;"> "Neg</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;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">4</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">6</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">4)}};</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" 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="LC509" 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;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">positive_site = {{"" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (1</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">((fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">filter_specification</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">partition</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">coverage</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">site</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC510" 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;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 1</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">10</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>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(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;">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;">10</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>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">3</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">10</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Pos</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;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">4</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">6</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">4)}};</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 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;">negative_site = {{"" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (1</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">((fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">filter_specification</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">partition</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">coverage</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">site</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC517" 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;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 1</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">10</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>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(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;">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;">10</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>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">3</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">10</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Neg</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;"> Format(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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">4</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">6</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">4)}};</span></span>
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<pre style="margin: 0;">+<span id="LC522" 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="LC523" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">function fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">echo (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;">site</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">row) {</span></span>
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<pre style="margin: 0;"> <span id="LC525" 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">@@ -477,21 +559,40 @@ lfunction fel.store_results (node, result, arguments) {</td>
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559
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC560" 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;">2</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="LC561" 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;">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="LC562" 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="LC563" 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;">ci") {</span></span>
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> result_row = { { 0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> // alpha</span></span>
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="brainfuck"><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;"> // beta</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="brainfuck"><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;"> // alpha==beta</span></span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="brainfuck"><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;"> // LRT</span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="brainfuck"><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;"> // 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>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="brainfuck"><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;"> // total branch length of tested branches</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="brainfuck"><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;"> // lower bound dN/dS</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="brainfuck"><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;"> // dN/dS MLE</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 0 // upper bound dN/dS</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } }; </span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> result_row = { { 0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> // alpha</span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="brainfuck"><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;"> // beta</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="brainfuck"><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;"> // alpha==beta</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> // LRT</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="brainfuck"><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;"> // 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>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="brainfuck"><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;"> // total branch length of tested branches</span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } };</span></span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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480
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583
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="brainfuck"></span>
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481
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> result_row = { { 0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> // alpha</span></span>
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482
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="brainfuck"><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;"> // beta</span></span>
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483
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="brainfuck"><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;"> // alpha==beta</span></span>
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484
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="brainfuck"><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;"> // LRT</span></span>
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="brainfuck"><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;"> // 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>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 0 // total branch length of tested branches</span></span>
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<pre style="margin: 0;">-<span id="LC487" 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="LC584" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (None != result) { // not a constant site</span></span>
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC587" 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="LC588" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> lrt = math</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">DoLRT ((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;">Null")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log_likelihood")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log_likelihood")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC590" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 1);</span></span>
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<pre style="margin: 0;">+<span id="LC591" 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="LC592" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (result / ^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">simulated") {</span></span>
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> pv = </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">((result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">simulated"</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;">"_MATRIX_ELEMENT_VALUE_</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;"> lrt </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LRT")</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="LC594" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> lrt </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p_value")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = (pv</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1)/(1</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;">resample");</span></span>
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<pre style="margin: 0;">+<span id="LC595" 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="LC596" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetGlobalMLE (result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_alpha");</span></span>
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetGlobalMLE (result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta");</span></span>
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598
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">2</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetGlobalMLE (result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta");</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">@@ -499,7 +600,6 @@ lfunction fel.store_results (node, result, arguments) {</td>
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600
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<pre style="margin: 0;"> <span id="LC600" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">4</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = lrt </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p_value")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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601
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="brainfuck"></span>
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602
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<pre style="margin: 0;"> <span id="LC602" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="brainfuck"></span>
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603
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<pre style="margin: 0;"> <span id="LC603" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sum = 0;</span></span>
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504
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604
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<pre style="margin: 0;"> <span id="LC604" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /*alternative_lengths = ((result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">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;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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605
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="brainfuck"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -511,6 +611,12 @@ lfunction fel.store_results (node, result, arguments) {</td>
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511
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611
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ');*/</span></span>
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612
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<pre style="margin: 0;"> <span id="LC612" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">5</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = sum;</span></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (None != result </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">confidence_interval"</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="LC616" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">6</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = (result </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">confidence_interval"</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;">lower_bound"</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="LC617" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">7</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = (result </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">confidence_interval"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MLE"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">8</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = (result </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">confidence_interval"</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;">upper_bound"</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="LC619" 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="LC620" 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="LC621" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC622" 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">@@ -588,8 +694,8 @@ for (fel.partition_index = 0; fel.partition_index < fel.partition_count; fel.par</td>
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<pre style="margin: 0;"> <span id="LC694" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC695" 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;">queue = mpi</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">CreateQueue ({"LikelihoodFunctions": {{"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_likelihood"}}</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC696" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Models" : {{"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mg_rev"}}</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Headers" : {{"libv3/all</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bf"}}</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC592" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Variables" : {{"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">srv"}}</span></span>
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Headers" : {{"libv3/all</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bf"</span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left">,</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">"libv3/tasks/alignments</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">bf"</span>}}</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Variables" : {{"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">srv"</span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left">,</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">resample"</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">"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">ci"</span>}}</span></span>
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<pre style="margin: 0;"> <span id="LC699" 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="LC700" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC701" 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">@@ -608,7 +714,8 @@ for (fel.partition_index = 0; fel.partition_index < fel.partition_count; fel.par</td>
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<pre style="margin: 0;"> <span id="LC714" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "1" : None</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC715" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "2" : fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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716
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "3" : _pattern_info_</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC611" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "4" : fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_model_mapping</span></span>
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "4" : fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_model_mapping</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "5" : 0</span></span>
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<pre style="margin: 0;"> <span id="LC719" 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="LC720" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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721
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> mpi</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">QueueJob (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">queue</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;">handle_a_site"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {"0" : "fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_likelihood"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -617,7 +724,8 @@ for (fel.partition_index = 0; fel.partition_index < fel.partition_count; fel.par</td>
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724
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<pre style="margin: 0;"> <span id="LC724" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (_pattern_info_</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sites")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC725" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "2" : fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "3" : _pattern_info_</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC620" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "4" : fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_model_mapping</span></span>
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "4" : fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_model_mapping</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "5" : 0</span></span>
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<pre style="margin: 0;"> <span id="LC729" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC730" 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;">store_results");</span></span>
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<pre style="margin: 0;"> <span id="LC731" 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">@@ -651,9 +759,12 @@ io.ReportProgressMessageMD ("fel", "results", "** Found _" + fel.report.counts[0</td>
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759
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<pre style="margin: 0;"> <span id="LC759" 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;">stopTimer (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">timers</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Total time");</span></span>
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760
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<pre style="margin: 0;"> <span id="LC760" 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;">stopTimer (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">timers</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "FEL analysis");</span></span>
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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 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;">resamples) {</span></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;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">simulated</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;">resamples;</span></span>
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">GetString (_hpv</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">HYPHY_VERSION</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="LC767" 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;">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;">runtime</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _hpv;</span></span>
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<pre style="margin: 0;"> <span id="LC768" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SpoolJSON (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="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;">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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#428ab1297972e0944fd35b5136d40326dd840dcb"><strong>res/TemplateBatchFiles/SelectionAnalyses/FUBAR.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">@@ -636,6 +636,9 @@ namespace fubar {</td>
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fubar</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;">fubar</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">grid</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = fubar</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">grid_with_weights;</span></span>
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<pre style="margin: 0;"> <span id="LC637" 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;">stopTimer (fubar</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;"> "Overall");</span></span>
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">GetString (_hpv</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">HYPHY_VERSION</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="LC640" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fubar</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;">runtime</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _hpv;</span></span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC642" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SpoolJSON (fubar</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;"> fubar</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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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<pre style="margin: 0;"> <span id="LC644" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">return fubar</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json;</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#af43f80c500c4a3acf886ebcfd048a6a7a3cf361"><strong>res/TemplateBatchFiles/SelectionAnalyses/FitMultiModel.bf</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -540,6 +540,10 @@ if (utility.Array1D (fitter.callout)) {</td>
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<pre style="margin: 0;"> <span id="LC540" 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="LC541" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReportProgressMessageMD ("fitter"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "writing"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Writing detailed analysis report to \`" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span 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="LC542" 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="LC543" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">GetString (_hpv</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">HYPHY_VERSION</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="LC544" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">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;">runtime</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _hpv;</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"></span></span>
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<pre style="margin: 0;">+<span id="LC546" 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="LC547" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SpoolJSON (fitter</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;"> fitter</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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">return fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json;</span></span>
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<pre style="margin: 0;"> <span id="LC549" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"></span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#bc98d7300147ce39ef8ee0f9b35f3252bebd01d2"><strong>res/TemplateBatchFiles/SelectionAnalyses/MEME.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">@@ -132,6 +132,10 @@ namespace meme {</td>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">pvalue = io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">PromptUser ("\n</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;">Select the p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">value threshold to use when testing for selection"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">pvalue</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">1</span><span 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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<pre style="margin: 0;"> <span id="LC134" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">KeywordArgument ("resample"</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;">Advanced setting</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> will result in MUCH SLOWER run time</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> Perform parametric bootstrap resampling to derive site</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">level null LRT distributions up to this many replicates per site</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> Recommended use for small to medium (</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">30 sequences) datasets"</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="LC136" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">resample = io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">PromptUser ("\n</span><span class="nb" style="color: #0086b3;">></span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">Advanced setting</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> will result in MUCH SLOWER run time</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> Perform parametric bootstrap resampling to derive site</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">level null LRT distributions up to this many replicates per site</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> Recommended use for small to medium (</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">30 sequences) datasets"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">50</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 class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">TRUE);</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="brainfuck"></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;">KeywordArgument ("output"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Write the resulting JSON to this file (default is to save to the same path as the alignment file </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 'MEME</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;"> meme</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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">PromptUserForFilePath ("Save the resulting JSON file to");</span></span>
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<pre style="margin: 0;"> <span id="LC141" 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">@@ -433,7 +437,7 @@ for (meme.partition_index = 0; meme.partition_index < meme.partition_count; meme</td>
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433
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437
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">queue = mpi</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">CreateQueue ({terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mpi</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LikelihoodFunctions: {{"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_likelihood"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_likelihood_bsrel"}}</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;">mpi</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Models : {{"meme</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;">background_fel"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bsrel"}}</span><span class="nf" style="color: #900; font-weight: 600;">,</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;">mpi</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Headers : utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetListOfLoadedModules ("libv3/")</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;">mpi</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Variables : {{"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">selected_branches"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_mixture"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">pairwise_counts"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon_data_info"}}</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;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mpi</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Variables : {{"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">selected_branches"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_mixture"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">pairwise_counts"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon_data_info"</span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left">,</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">"meme</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">resample"</span>}}</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;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mpi</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Functions : {{"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">compute_branch_EBF"}}</span></span>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> });</span></span>
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="brainfuck"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -452,7 +456,8 @@ for (meme.partition_index = 0; meme.partition_index < meme.partition_count; meme</td>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "2" : None</span><span class="nf" style="color: #900; font-weight: 600;">,</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;"> "3" : meme</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>
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "4" : _pattern_info_</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;"> "5" : meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_model_mapping</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;"> "5" : meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_model_mapping</span><span class="nf" style="color: #900; font-weight: 600;">,</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;"> "6" : 0</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;"> mpi</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">QueueJob (meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">queue</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">handle_a_site"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {"0" : "meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_likelihood"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -462,7 +467,8 @@ for (meme.partition_index = 0; meme.partition_index < meme.partition_count; meme</td>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (_pattern_info_</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sites")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "3" : meme</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>
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "4" : _pattern_info_</span><span class="nf" style="color: #900; font-weight: 600;">,</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;"> "5" : meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_model_mapping</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;"> "5" : meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_model_mapping</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "6" : 0</span></span>
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<pre style="margin: 0;"> <span id="LC472" 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="LC473" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">store_results");</span></span>
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<pre style="margin: 0;"> <span id="LC474" 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">@@ -496,6 +502,10 @@ io.ReportProgressMessageMD ("MEME", "results", "** Found _" + meme.report.count[</td>
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<pre style="margin: 0;"> <span id="LC502" 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;">stopTimer (meme</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;"> "Total time");</span></span>
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497
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503
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">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;">stopTimer (meme</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;"> "MEME analysis");</span></span>
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498
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504
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="brainfuck"></span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">GetString (_hpv</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">HYPHY_VERSION</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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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">meme</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;">runtime</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _hpv;</span></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="brainfuck"></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="brainfuck"></span>
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499
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509
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SpoolJSON (meme</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;"> meme</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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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500
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510
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="brainfuck"></span>
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501
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511
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">//</span><span class="nf" style="color: #900; font-weight: 600;">----------------------------------------------------------------------------------------</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="571" style="width: 35px; color: rgba(0,0,0,0.3); 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="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -571,7 +581,7 @@ lfunction meme.compute_branch_EBF (lf_id, tree_name, branch_name, baseline) {</td>
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571
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581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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572
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582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="brainfuck"></span>
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573
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583
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<pre style="margin: 0;"> <span id="LC583" 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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574
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">handle_a_site (lf_fel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> lf_bsrel</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>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">handle_a_site (lf_fel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> lf_bsrel</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 class="idiff left">,</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"> sim_mode</span>) {</span></span>
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575
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585
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="brainfuck"></span>
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576
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586
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //console</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log (pattern_info);</span></span>
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577
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587
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //#profile START;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -706,92 +716,94 @@ lfunction meme.handle_a_site (lf_fel, lf_bsrel, filter_data, partition_index, pa</td>
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<pre style="margin: 0;"> <span id="LC716" 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="LC717" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //alternative = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ExtractMLEs (lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping);</span></span>
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<pre style="margin: 0;">-<span id="LC709" 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_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">globals_only" : TRUE});</span></span>
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<pre style="margin: 0;">-<span id="LC710" 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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<pre style="margin: 0;">-<span id="LC711" class="line" lang="brainfuck"></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;"> /*init_grid_best = ^"LF_INITIAL_GRID_MAXIMUM";</span></span>
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<pre style="margin: 0;">-<span id="LC713" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (Abs((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="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">init_grid_best)/results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">05) {</span></span>
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<pre style="margin: 0;">-<span id="LC714" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> console</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log (before_opt);</span></span>
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<pre style="margin: 0;">-<span id="LC715" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> console</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log (^"LF_INITIAL_GRID_MAXIMUM_VALUE");</span></span>
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<pre style="margin: 0;">-<span id="LC716" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> console</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log (after_opt);</span></span>
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<pre style="margin: 0;">-<span id="LC717" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> console</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log ("" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> " vs " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> init_grid_best);</span></span>
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<pre style="margin: 0;">-<span id="LC718" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC719" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //fprintf (stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\n");</span></span>
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<pre style="margin: 0;">-<span id="LC720" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetEnvVariable ("VERBOSITY_LEVEL"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">10);</span></span>
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<pre style="margin: 0;">-<span id="LC721" 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="LC719" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (sim_mode) {</span></span>
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> lrt = 2*results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">; </span></span>
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<pre style="margin: 0;">+<span id="LC721" 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="LC722" 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_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">globals_only" : TRUE});</span></span>
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<pre style="margin: 0;">+<span id="LC723" 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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<pre style="margin: 0;">+<span id="LC724" 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_bsrel</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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<pre style="margin: 0;">+<span id="LC725" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //TODO</span></span>
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 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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<pre style="margin: 0;">+<span id="LC727" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> DeleteObject (ancestral_info);</span></span>
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> branch_ebf = {};</span></span>
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> branch_posterior = {};</span></span>
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<pre style="margin: 0;"> <span id="LC731" 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="LC723" 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="LC724" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC725" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> console</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log ("</span><span class="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="LC732" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC733" 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="LC734" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC728" 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_bsrel</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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<pre style="margin: 0;"> <span id="LC735" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC730" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //TODO</span></span>
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<pre style="margin: 0;">-<span id="LC731" 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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<pre style="margin: 0;">-<span id="LC732" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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736
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<pre style="margin: 0;"> <span id="LC736" class="line" lang="brainfuck"></span>
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734
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<pre style="margin: 0;">-<span id="LC734" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> DeleteObject (ancestral_info);</span></span>
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735
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<pre style="margin: 0;">-<span id="LC735" class="line" lang="brainfuck"></span>
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736
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<pre style="margin: 0;">-<span id="LC736" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> branch_ebf = {};</span></span>
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737
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<pre style="margin: 0;">-<span id="LC737" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> branch_posterior = {};</span></span>
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738
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737
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<pre style="margin: 0;"> <span id="LC737" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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739
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738
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<pre style="margin: 0;"> <span id="LC738" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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740
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739
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<pre style="margin: 0;"> <span id="LC739" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta_plus" </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;"> ^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_alpha" && ^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_mixture_weight" </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">999999) {</span></span>
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741
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<pre style="margin: 0;">-<span id="LC741" class="line" lang="brainfuck"></span>
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742
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<pre style="margin: 0;">-<span id="LC742" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /*</span></span>
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743
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<pre style="margin: 0;">-<span id="LC743" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_tree_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">aipysurusLaevis</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha" </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;"> 10000) {</span></span>
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744
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<pre style="margin: 0;">-<span id="LC744" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Export (lfe</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf_bsrel);</span></span>
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745
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<pre style="margin: 0;">-<span id="LC745" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> console</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log (lfe);</span></span>
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746
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<pre style="margin: 0;">-<span id="LC746" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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747
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<pre style="margin: 0;">-<span id="LC747" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> */</span></span>
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748
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<pre style="margin: 0;">-<span id="LC748" class="line" lang="brainfuck"></span>
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749
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<pre style="margin: 0;">-<span id="LC749" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> LFCompute (^lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">LF_START_COMPUTE);</span></span>
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750
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<pre style="margin: 0;">-<span id="LC750" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> LFCompute (^lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">baseline);</span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (!sim_mode) { </span></span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> LFCompute (^lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">LF_START_COMPUTE);</span></span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> LFCompute (^lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">baseline);</span></span>
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751
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<pre style="margin: 0;"> <span id="LC743" 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="LC744" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC753" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (_node_name_; in; ^bsrel_tree_id) {</span></span>
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<pre style="margin: 0;">-<span id="LC754" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (((^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">selected_branches") </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> == utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">tree_attributes</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test")) {</span></span>
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<pre style="margin: 0;">-<span id="LC755" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _node_name_res_ = meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">compute_branch_EBF (lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> bsrel_tree_id</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _node_name_</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> baseline);</span></span>
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<pre style="margin: 0;">-<span id="LC756" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> branch_ebf</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _node_name_res_</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">empirical_bayes_factor")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">-<span id="LC757" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> branch_posterior</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _node_name_res_</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">posterior")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (_node_name_; in; ^bsrel_tree_id) {</span></span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (((^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">selected_branches") </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> == utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">tree_attributes</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test")) {</span></span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _node_name_res_ = meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">compute_branch_EBF (lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> bsrel_tree_id</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _node_name_</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> baseline);</span></span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> branch_ebf</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _node_name_res_</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">empirical_bayes_factor")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> branch_posterior</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _node_name_res_</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">posterior")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">+<span id="LC750" 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="LC751" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC759" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC752" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC753" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC762" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> LFCompute (^lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">LF_DONE_COMPUTE);</span></span>
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> LFCompute (^lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">LF_DONE_COMPUTE);</span></span>
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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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;"> ^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta_plus" := ^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_alpha";</span></span>
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758
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<pre style="margin: 0;"> <span id="LC758" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Optimize (results</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {"OPTIMIZATION_METHOD" : "nedler</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">mead"});</span></span>
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759
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<pre style="margin: 0;"> <span id="LC759" 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;">SpoolLF (lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "/tmp/meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><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;"> "MEME</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">null");</span></span>
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760
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="brainfuck"></span>
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761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //Null = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ExtractMLEs (lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping);</span></span>
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<pre style="margin: 0;">-<span id="LC769" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Null = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ExtractMLEsOptions (lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">globals_only" : TRUE});</span></span>
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<pre style="margin: 0;">-<span id="LC770" class="line" lang="brainfuck"></span>
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771
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<pre style="margin: 0;">-<span id="LC771" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Null </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log_likelihood")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">-<span id="LC772" class="line" lang="brainfuck"></span>
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762
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="brainfuck"></span>
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763
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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 (sim_mode) {</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;"> return lrt </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> 2*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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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else { </span></span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Null = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ExtractMLEsOptions (lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">globals_only" : TRUE});</span></span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Null </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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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;"> if (^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">resample") {</span></span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> N = ^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">resample";</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sims = {};</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;"> GetDataInfo (fi</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^((lfInfo</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"Datafilters"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "PARAMETERS");</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (i = 0; i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> N; i</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">=1) { </span></span>
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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;"> DataSet null_sim = SimulateDataSet (^lf_bsrel);</span></span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> DataSetFilter null_filter = CreateFilter (null_sim</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;">fi</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"EXCLUSIONS"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></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;"> sims </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">serialize_site_filter (&null_filter</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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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;"> }</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;"> null_LRT = {N</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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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;"> for (i = 0; i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> N; i</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">=1) { </span></span>
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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;"> is = meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">handle_a_site (lf_fel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> sims</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 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;"> TRUE);</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;"> null_LRT</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;"> = is;</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;"> }</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;"> </span></span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return {"fel" : fel</span><span class="nf" style="color: #900; font-weight: 600;">,</span></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;"> 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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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;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">posterior") : branch_posterior</span><span class="nf" style="color: #900; font-weight: 600;">,</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;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">empirical_bayes_factor") : branch_ebf</span><span class="nf" style="color: #900; font-weight: 600;">,</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;"> 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 class="c1" style="color: #998; font-style: italic;"> //TODO: keep this attr?</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;"> 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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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;"> 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;">simulated"): null_LRT</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 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>
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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;"> } else {</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;"> Null = alternative;</span></span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (!sim_mode) {</span></span>
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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Null = alternative;</span></span>
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777
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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;"> </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;"> for (_node_name_; in; ^bsrel_tree_id) {</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;"> if (((^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">selected_branches") </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> == utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">tree_attributes</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test")) {</span></span>
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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;"> branch_ebf</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = 1</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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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;"> branch_posterior</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = 0</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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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;"> }</span></span>
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783
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<pre style="margin: 0;">-<span id="LC783" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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784
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<td class="new_line diff-line-num old" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="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;"> /*</span></span>
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786
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<td class="new_line diff-line-num old" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC786" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ForEach (^bsrel_tree_id</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_node_name_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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787
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<td class="new_line diff-line-num old" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC787" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> '</span></span>
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788
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<td class="new_line diff-line-num old" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC788" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if ((meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">selected_branches </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"`&partition_index`"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> == utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">tree_attributes</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test")) {</span></span>
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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;"> (^"`&branch_ebf`")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = 1</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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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;"> (^"`&branch_posterior`")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = 0</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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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;"> for (_node_name_; in; ^bsrel_tree_id) {</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;"> if (((^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">selected_branches") </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> == utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">tree_attributes</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test")) {</span></span>
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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;"> branch_ebf</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = 1</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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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;"> branch_posterior</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = 0</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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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 class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC792" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right">'</span></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 class="idiff left right">)</span>;</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 class="idiff left right">*/</span></span></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;"> <span class="idiff left right">} else {</span></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;"> <span class="idiff left right"> return 0</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC806" 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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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;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC808" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC809" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //#profile collect;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="913" style="width: 35px; color: rgba(0,0,0,0.3); 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="925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -913,6 +925,12 @@ lfunction meme.store_results (node, result, arguments) {</td>
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<pre style="margin: 0;"> <span id="LC925" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC926" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> lrt = {utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LRT") : 2*((result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log_likelihood")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">(result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log_likelihood")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)};</span></span>
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<pre style="margin: 0;"> <span id="LC927" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> lrt </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p_value")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = 2/3</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">2/3*(0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">45*CChi2(lrt</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LRT")</span><span class="p">]</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;">55*CChi2(lrt</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LRT")</span><span class="p">]</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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<pre style="margin: 0;">+<span id="LC928" 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="LC929" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (result / ^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">simulated") {</span></span>
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930
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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931
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> pv = </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">((result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">simulated"</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;">"_MATRIX_ELEMENT_VALUE_</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;"> lrt </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LRT")</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> lrt </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p_value")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = (pv</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1)/(1</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">resample");</span></span>
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933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } </span></span>
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934
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<pre style="margin: 0;"> <span id="LC934" class="line" lang="brainfuck"></span>
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935
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<pre style="margin: 0;"> <span id="LC935" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetGlobalMLE (result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameter_site_alpha"));</span></span>
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936
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<pre style="margin: 0;"> <span id="LC936" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetGlobalMLE (result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameter_site_omega_minus")) * result_row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#80cb7c212661a2afbd05c16dce9f84f45709578e"><strong>res/TemplateBatchFiles/SelectionAnalyses/PRIME.bf</strong></a>
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<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">@@ -537,6 +537,10 @@ for (key, value; in; prime.report.count) {</td>
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<pre style="margin: 0;"> <span id="LC537" 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;">stopTimer (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;"> "Total time");</span></span>
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538
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<pre style="margin: 0;"> <span id="LC538" 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;">stopTimer (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;"> "PRIME analysis");</span></span>
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">GetString (_hpv</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">HYPHY_VERSION</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="LC541" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">runtime</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _hpv;</span></span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SpoolJSON (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="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_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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC546" 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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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#cf5243a3058ebeab74574f8cd2c771cd63a43208"><strong>res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -41,7 +41,8 @@ relax.analysis_description = {</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Version 3 provides support for </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;">2 branch sets</span><span class="nf" style="color: #900; font-weight: 600;">.</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Version 3</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">1 adds LHC </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> Nedler</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">Mead initial fit phase and keyword support</span><span class="nf" style="color: #900; font-weight: 600;">.</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Version 3</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">1 adds some bug fixes for better convergence</span><span class="nf" style="color: #900; font-weight: 600;">.</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Version 4</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">0 adds support for synonymous rate variation</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Version 4</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">0 adds support for synonymous rate variation</span><span class="nf" style="color: #900; font-weight: 600;">.</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Version 4</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">1 adds further support for multiple hit models"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">version : "3</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">1"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">reference : "RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015)</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> Mol Biol Evol 32 (3): 820</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">832"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">authors : "Sergei L Kosakovsky Pond</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Ben Murrell</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Steven Weaver and Temple iGEM / UCSD viral evolution group"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -140,8 +141,6 @@ KeywordArgument ("test", "Branches to use as the test set", null, "Choose the s</td>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">KeywordArgument ("reference"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Branches to use as the reference set"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> null</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Choose the set of branches to use as the _reference_ set");</span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC144" 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;">DisplayAnalysisBanner ( relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">analysis_description );</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">selection</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">startTimer (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">timers</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Overall"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -163,6 +162,15 @@ relax.N.initial_guesses = io.PromptUser ("The number of initial random guesses t</td>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReportProgressMessageMD('RELAX'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 'selector'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 'Branch sets for RELAX analysis');</span></span>
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="brainfuck"></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">KeywordArgument ("multiple</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">hits"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Include support for multiple nucleotide substitutions"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "None");</span></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">multi_hit = io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SelectAnOption ({</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"Double"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Include branch</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">specific rates for double nucleotide substitutions"}</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"Double</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">Triple"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Include branch</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">specific rates for double and triple nucleotide substitutions"}</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"None"</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;">Default</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> Use standard models which permit only single nucleotide changes to occur instantly"}</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Include support for multiple nucleotide substitutions");</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="brainfuck"></span>
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="brainfuck"></span>
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">numbers_of_tested_groups == 2) {</span></span>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_sets = {relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test_branches_name : "test"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -313,32 +321,86 @@ utility.ForEachPair (relax.filter_specification, "_key_", "_value_",</td>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_generator = "models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ModelDescription";</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">multi_hit == "None") {</span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_generator = "models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ModelDescription";</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">do_srv) {</span></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">do_bs_srv) {</span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_generator = "relax</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;">with</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GDD";</span></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_generator = "models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL_SRV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ModelDescription";</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_class_arguments = {{relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate_classes__</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_classes__}};</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">do_srv) {</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">do_bs_srv) {</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_generator = "models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL_SRV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ModelDescription";</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_class_arguments = {{relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate_classes__</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_classes__}};</span></span>
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<pre style="margin: 0;">+<span id="LC331" 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="LC332" 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="LC325" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> lfunction relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">with</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GDD (type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> code</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> rates) { </span></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> def = models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ModelDescription (type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> code</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> rates);</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> options = {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;">rate_variation</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bins") : utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate_classes")</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC328" 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;">_namespace") : "relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_shared_srv"};</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>lfunction relax</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;">with</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GDD (type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> code</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> rates) { </span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>def = models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ModelDescription (type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> code</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> rates);</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>options = {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;">rate_variation</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bins") : utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate_classes")</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>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;">_namespace") : "relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_shared_srv"};</span></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">do_srv_hmm")) {</span></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> options </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue ("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_variation</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">HMM")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = "equal";</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">do_srv_hmm")) {</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> options </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue ("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_variation</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">HMM")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = "equal";</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> def </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_variation")</span><span class="p">]</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;">types</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GDD</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">factory (options);</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return def;</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> def </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_variation")</span><span class="p">]</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;">types</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GDD</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">factory (options);</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return def;</span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_generator = "relax</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;">with</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GDD";</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_generator = "relax</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;">with</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GDD";</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_class_arguments = relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_classes;</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC348" 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="LC349" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_class_arguments = relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_classes;</span></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC351" 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="LC341" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_class_arguments = relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_classes;</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> lfunction relax</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;">BS_REL_MH (type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> code</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> rates) { </span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> def = models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ModelDescription (type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> code</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> rates);</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> def </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">defineQ")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = "models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_DefineQ</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MH";</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (^'relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">multi_hit' == "Double") {</span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> def </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_generator")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = "function rate_generator (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model) {</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV_MH</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_GenerateRate_generic (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">translation_table')</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="brainfuck"><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;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'beta_' </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> component</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">nonsynonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'omega' </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> component</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">omega_ratio')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'delta'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">multiple_hit_rate')</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" 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="LC364" 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="LC365" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> def </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_generator")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = "function rate_generator (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model) {</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV_TRIP</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_GenerateRate_generic (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">translation_table')</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="brainfuck"><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;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'beta_' </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> component</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">nonsynonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'omega' </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> component</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">omega_ratio')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'delta'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">multiple_hit_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'psi'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">triple_hit_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'psi'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">triple_hit_rate')</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> );}" </span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } </span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return def;</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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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;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_generator = "relax</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;">BS_REL_MH";</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">do_srv) {</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">do_bs_srv) {</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_generator = "models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL_SRV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ModelDescription";</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_class_arguments = {{relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate_classes__</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_classes__}};</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> lfunction relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">with</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GDD (type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> code</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> rates) { </span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> def = relax</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;">BS_REL_MH (type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> code</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> rates);</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> options = {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;">rate_variation</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bins") : utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate_classes")</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 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;">_namespace") : "relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_shared_srv"};</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="brainfuck"></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">do_srv_hmm")) {</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;"> options </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue ("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_variation</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">HMM")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = "equal";</span></span>
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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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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> def </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_variation")</span><span class="p">]</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;">types</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GDD</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">factory (options);</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return def;</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_generator = "relax</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;">with</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GDD";</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_class_arguments = relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_classes;</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_class_arguments = relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_classes;</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" 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="LC404" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="brainfuck"></span>
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406
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<pre style="margin: 0;"> <span id="LC406" 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;">stopTimer (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">timers</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Preliminary model fitting");</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -367,7 +429,6 @@ if (relax.model_set == "All") { // run all the models</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;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">weight_multipliers = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">helper</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">stick_breaking (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SwapKeysAndValues(utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MatrixToDict(relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">distribution</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"weights"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">))</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">None);</span></span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">constrain_parameters = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ConstrainMeanOfSet(relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">distribution</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"rates"</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">weight_multipliers</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;">"relax");</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="LC370" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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432
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i = 0;</span></span>
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433
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (key</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> value; in; relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">constrain_parameters</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">global</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">){</span></span>
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434
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddGlobal (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ge</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="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;"> key);</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">@@ -509,6 +570,9 @@ if (relax.model_set == "All") { // run all the models</td>
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570
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "{terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">omega_ratio : relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">inferred_ge_distribution </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_index_</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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571
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">proportion : relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">inferred_ge_distribution </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_index_</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">}")</span></span>
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<pre style="margin: 0;"> <span id="LC572" 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="LC573" 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="LC574" 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="LC575" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report_multi_hit (elax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">general_descriptive</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">distribution_for_json</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "RELAX"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "gd</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">mh");</span></span>
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> selection</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json_store_lf (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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577
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">general_descriptive_name</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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578
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">general_descriptive</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log_likelihood</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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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">@@ -571,7 +635,6 @@ if (relax.numbers_of_tested_groups == 2) {</td>
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_for_srv = "relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test";</span></span>
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC637" 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="LC574" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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638
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_to_group_name = {};</span></span>
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639
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_namespaces = {};</span></span>
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640
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<pre style="margin: 0;"> <span id="LC640" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ForEachPair (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_sets</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_key_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_value_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "</span></span>
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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">@@ -695,9 +758,6 @@ if (relax.do_srv) {</td>
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758
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<pre style="margin: 0;"> <span id="LC758" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_set != "All") {</span></span>
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<pre style="margin: 0;">-<span id="LC698" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /*</span></span>
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<pre style="margin: 0;">-<span id="LC699" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ge_guess = relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">DistributionGuess(((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;">extract_global_MLE_re (relax</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;"> "^" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">omega_ratio </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;">`relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test_branches_name`</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;">"0"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MLE</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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<pre style="margin: 0;">-<span id="LC700" 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="LC761" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">do_lhc = TRUE;</span></span>
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702
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762
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">distribution = models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ExtractMixtureDistribution(relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_object_map</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">reference_model_namespace</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="LC763" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">initial</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test_mean = ((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;">extract_global_MLE_re (relax</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;"> "^" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">omega_ratio </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;">`relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test_branches_name`</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;">"0"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MLE</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -963,17 +1023,17 @@ function relax.FitMainTestPair () {</td>
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963
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1023
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<pre style="margin: 0;"> <span id="LC1023" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "{terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">omega_ratio : relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">inferred_distribution </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_index_</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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964
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1024
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<pre style="margin: 0;"> <span id="LC1024" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">proportion : relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">inferred_distribution </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_index_</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">1</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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965
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1025
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<pre style="margin: 0;"> <span id="LC1025" class="line" lang="brainfuck"></span>
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966
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<td class="new_line diff-line-num old" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC966" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">reference_branches_name : utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Map (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Range (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_classes</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 1)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">reference_branches_name : utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Map (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Range (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_classes</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 1)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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967
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1027
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<pre style="margin: 0;"> <span id="LC1027" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "_index_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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968
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1028
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<pre style="margin: 0;"> <span id="LC1028" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "{terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">omega_ratio : relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">inferred_distribution_ref </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_index_</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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969
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1029
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<pre style="margin: 0;"> <span id="LC1029" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">proportion : relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">inferred_distribution_ref </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_index_</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">}")</span></span>
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1030
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<pre style="margin: 0;"> <span id="LC1030" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> };</span></span>
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1031
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<pre style="margin: 0;"> <span id="LC1031" class="line" lang="brainfuck"></span>
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1032
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<pre style="margin: 0;"> <span id="LC1032" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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973
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<pre style="margin: 0;">-<span id="LC973" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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974
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1033
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<pre style="margin: 0;"> <span id="LC1033" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report_multi_class_rates (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> TRUE);</span></span>
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975
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1034
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<pre style="margin: 0;"> <span id="LC1034" 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="LC976" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC1035" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="1036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1036
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<pre style="margin: 0;">+<span id="LC1036" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report_multi_hit (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">distribution_for_json</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "RELAX"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "alt</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">mh");</span></span>
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977
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<td class="new_line diff-line-num" data-linenumber="1037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1037
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<pre style="margin: 0;"> <span id="LC1037" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_report_srv (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> FALSE);</span></span>
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978
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<td class="new_line diff-line-num" data-linenumber="1038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1038
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<pre style="margin: 0;"> <span id="LC1038" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<td class="old_line diff-line-num" data-linenumber="979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
979
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1039
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<pre style="margin: 0;"> <span id="LC1039" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> KeywordArgument ("save</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">fit"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Save RELAX alternative model fit to this file (default is not to save)"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "/dev/null");</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); 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="1089" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1029,6 +1089,7 @@ function relax.FitMainTestPair () {</td>
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1029
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<td class="new_line diff-line-num" data-linenumber="1089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1089
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<pre style="margin: 0;"> <span id="LC1089" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report_multi_class_rates (None</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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1030
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1090
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<pre style="margin: 0;"> <span id="LC1090" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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1031
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1091
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<pre style="margin: 0;"> <span id="LC1091" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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1092
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<pre style="margin: 0;">+<span id="LC1092" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report_multi_hit (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">null_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">distribution_for_json</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "RELAX"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "alt</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">mh</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">null");</span></span>
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1032
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1093
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<pre style="margin: 0;"> <span id="LC1093" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_report_srv (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">null_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> TRUE);</span></span>
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1033
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1094
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<pre style="margin: 0;"> <span id="LC1094" class="line" lang="brainfuck"></span>
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1034
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1095
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<pre style="margin: 0;"> <span id="LC1095" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> selection</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json_store_lf (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1140" style="width: 35px; color: rgba(0,0,0,0.3); 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="1201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1140,6 +1201,7 @@ if (relax.model_set == "All") {</td>
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1140
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1201
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<pre style="margin: 0;"> <span id="LC1201" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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1141
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<td class="new_line diff-line-num" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1202
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<pre style="margin: 0;"> <span id="LC1202" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report_multi_class_rates (None</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> TRUE);</span></span>
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1142
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1203
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<pre style="margin: 0;"> <span id="LC1203" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1204
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<pre style="margin: 0;">+<span id="LC1204" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report_multi_hit (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">pe</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">distribution_for_json</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "RELAX"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "pe</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">mh");</span></span>
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1143
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1205
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<pre style="margin: 0;"> <span id="LC1205" class="line" lang="brainfuck"></span>
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1144
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1206
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<pre style="margin: 0;"> <span id="LC1206" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> selection</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json_store_lf (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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1145
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1207
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<pre style="margin: 0;"> <span id="LC1207" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partitioned_descriptive_name</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1160,6 +1222,10 @@ if (relax.model_set == "All") {</td>
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1160
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1222
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<pre style="margin: 0;"> <span id="LC1222" class="line" lang="brainfuck"></span>
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1161
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1223
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<pre style="margin: 0;"> <span id="LC1223" 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;">stopTimer (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">timers</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Overall");</span></span>
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1162
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1224
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<pre style="margin: 0;"> <span id="LC1224" class="line" lang="brainfuck"></span>
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1225
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<pre style="margin: 0;">+<span id="LC1225" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">GetString (_hpv</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">HYPHY_VERSION</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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1226
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<pre style="margin: 0;">+<span id="LC1226" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="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;">runtime</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _hpv;</span></span>
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1227
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<pre style="margin: 0;">+<span id="LC1227" class="line" lang="brainfuck"></span>
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1228
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<pre style="margin: 0;">+<span id="LC1228" class="line" lang="brainfuck"></span>
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1163
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1229
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<pre style="margin: 0;"> <span id="LC1229" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SpoolJSON (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon_data_info </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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1164
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1230
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<pre style="margin: 0;"> <span id="LC1230" class="line" lang="brainfuck"></span>
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1165
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1231
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<pre style="margin: 0;"> <span id="LC1231" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">return relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1253" style="width: 35px; color: rgba(0,0,0,0.3); 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="1319" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1253,6 +1319,103 @@ lfunction relax.DistributionGuess (mean) {</td>
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1253
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1319
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<pre style="margin: 0;"> <span id="LC1319" class="line" lang="brainfuck"></span>
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1254
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1320
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<pre style="margin: 0;"> <span id="LC1320" 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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1255
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1321
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<pre style="margin: 0;"> <span id="LC1321" class="line" lang="brainfuck"></span>
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1322
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<pre style="margin: 0;">+<span id="LC1322" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_GenerateRate</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MH (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _tt</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;"> alpha_term</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;"> beta_term</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> omega</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> omega_term</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> delta</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> delta_term</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> psi</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> psi_term</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> psi_s</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> psi_s_term) {</span></span>
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1323
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<pre style="margin: 0;">+<span id="LC1323" class="line" lang="brainfuck"></span>
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1324
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<pre style="margin: 0;">+<span id="LC1324" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> p = {};</span></span>
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1325
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<pre style="margin: 0;">+<span id="LC1325" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _GenerateRate</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">diff = models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">diff</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">complete(fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar);</span></span>
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1326
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<pre style="margin: 0;">+<span id="LC1326" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> diff_count = utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Array1D (_GenerateRate</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">diff);</span></span>
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1327
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<pre style="margin: 0;">+<span id="LC1327" class="line" lang="brainfuck"></span>
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1328
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<pre style="margin: 0;">+<span id="LC1328" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (diff_count </span></span>
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1329
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<pre style="margin: 0;">+<span id="LC1329" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ) {</span></span>
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1330
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<pre style="margin: 0;">+<span id="LC1330" class="line" lang="brainfuck"></span>
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1331
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<pre style="margin: 0;">+<span id="LC1331" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> p</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">model_type</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = {};</span></span>
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1332
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<pre style="margin: 0;">+<span id="LC1332" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> p</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">global")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = {};</span></span>
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1333
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<pre style="margin: 0;">+<span id="LC1333" class="line" lang="brainfuck"></span>
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1334
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<pre style="margin: 0;">+<span id="LC1334" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> nuc_rate = "";</span></span>
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1335
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<pre style="margin: 0;">+<span id="LC1335" class="line" lang="brainfuck"></span>
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1336
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<pre style="margin: 0;">+<span id="LC1336" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (i = 0; i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> diff_count; i </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1) {</span></span>
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1337
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<pre style="margin: 0;">+<span id="LC1337" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if ((_GenerateRate</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">diff</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="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;">diff</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">from")</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;"> (_GenerateRate</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">diff</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="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;">diff</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">to")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) {</span></span>
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1338
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<pre style="margin: 0;">+<span id="LC1338" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> nuc_p = "theta_" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (_GenerateRate</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">diff</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="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;">diff</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">to")</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;"> (_GenerateRate</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">diff</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="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;">diff</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">from")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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1339
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<pre style="margin: 0;">+<span id="LC1339" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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1340
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<pre style="margin: 0;">+<span id="LC1340" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> nuc_p = "theta_" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (_GenerateRate</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">diff</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="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;">diff</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">from")</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;">(_GenerateRate</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">diff</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="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;">diff</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">to")</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="LC1341" 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="LC1342" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> nuc_p = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ApplyNameSpace(nuc_p</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace);</span></span>
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1343
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<pre style="margin: 0;">+<span id="LC1343" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (p</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">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;">nucleotideRateReversible((_GenerateRate</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">diff</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="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;">diff</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">from")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> (_GenerateRate</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">diff</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="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;">diff</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">to")</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;"> = nuc_p;</span></span>
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1344
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<pre style="margin: 0;">+<span id="LC1344" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC1345" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> nuc_rate = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AppendMultiplicativeTerm (nuc_rate</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> nuc_p);</span></span>
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1346
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<pre style="margin: 0;">+<span id="LC1346" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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1347
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<pre style="margin: 0;">+<span id="LC1347" class="line" lang="brainfuck"></span>
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1348
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<pre style="margin: 0;">+<span id="LC1348" class="line" lang="brainfuck"></span>
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1349
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<pre style="margin: 0;">+<span id="LC1349" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rate_entry = nuc_rate;</span></span>
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1350
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<pre style="margin: 0;">+<span id="LC1350" class="line" lang="brainfuck"></span>
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1351
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<pre style="margin: 0;">+<span id="LC1351" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (_tt</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fromChar</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> != _tt</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">toChar</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) {</span></span>
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1352
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<pre style="margin: 0;">+<span id="LC1352" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (model_type == utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">global")) {</span></span>
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1353
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<pre style="margin: 0;">+<span id="LC1353" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> aa_rate = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ApplyNameSpace(omega</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace);</span></span>
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1354
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<pre style="margin: 0;">+<span id="LC1354" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (p</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">model_type</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">omega_term</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = aa_rate;</span></span>
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1355
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<pre style="margin: 0;">+<span id="LC1355" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">EnsureKey (p</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">local"));</span></span>
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1356
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<pre style="margin: 0;">+<span id="LC1356" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (p</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">local")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue ("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">k")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = "k";</span></span>
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1357
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<pre style="margin: 0;">+<span id="LC1357" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> aa_rate </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= "^k";</span></span>
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1358
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<pre style="margin: 0;">+<span id="LC1358" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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1359
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<pre style="margin: 0;">+<span id="LC1359" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> aa_rate = beta;</span></span>
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1360
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<pre style="margin: 0;">+<span id="LC1360" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (p</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">model_type</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">beta_term</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = aa_rate;</span></span>
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1361
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<pre style="margin: 0;">+<span id="LC1361" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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1362
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<pre style="margin: 0;">+<span id="LC1362" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rate_entry </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= "*" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> aa_rate;</span></span>
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1363
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<pre style="margin: 0;">+<span id="LC1363" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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1364
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<pre style="margin: 0;">+<span id="LC1364" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (model_type == utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">local")) {</span></span>
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1365
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<pre style="margin: 0;">+<span id="LC1365" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (p</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">model_type</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">alpha_term</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = alpha;</span></span>
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1366
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<pre style="margin: 0;">+<span id="LC1366" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rate_entry </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= "*" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> alpha;</span></span>
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1367
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<pre style="margin: 0;">+<span id="LC1367" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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1368
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<pre style="margin: 0;">+<span id="LC1368" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> p</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_entry")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = nuc_rate;</span></span>
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1369
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<pre style="margin: 0;">+<span id="LC1369" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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1370
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<pre style="margin: 0;">+<span id="LC1370" class="line" lang="brainfuck"></span>
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1371
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<pre style="margin: 0;">+<span id="LC1371" class="line" lang="brainfuck"></span>
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1372
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<pre style="margin: 0;">+<span id="LC1372" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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1373
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<pre style="margin: 0;">+<span id="LC1373" class="line" lang="brainfuck"></span>
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1374
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<pre style="margin: 0;">+<span id="LC1374" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (diff_count == 2) {</span></span>
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1375
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<pre style="margin: 0;">+<span id="LC1375" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (model_type == utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">global")) {</span></span>
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1376
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<pre style="margin: 0;">+<span id="LC1376" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> delta_rate = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ApplyNameSpace(delta</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace);</span></span>
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1377
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<pre style="margin: 0;">+<span id="LC1377" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (p</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">model_type</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">delta_term</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = delta_rate;</span></span>
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1378
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<pre style="margin: 0;">+<span id="LC1378" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rate_entry </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= "*" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> delta_rate;</span></span>
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1379
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<pre style="margin: 0;">+<span id="LC1379" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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1380
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<pre style="margin: 0;">+<span id="LC1380" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (p</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">model_type</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">delta_term</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = delta;</span></span>
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1381
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<pre style="margin: 0;">+<span id="LC1381" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rate_entry </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= "*" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> delta;</span></span>
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1382
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<pre style="margin: 0;">+<span id="LC1382" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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1383
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<pre style="margin: 0;">+<span id="LC1383" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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1384
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<pre style="margin: 0;">+<span id="LC1384" class="line" lang="brainfuck"></span>
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1385
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<pre style="margin: 0;">+<span id="LC1385" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="1386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1386
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<pre style="margin: 0;">+<span id="LC1386" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (diff_count == 3 && ^'relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">multi_hit' == 'Double</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">Triple') {</span></span>
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1387
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<pre style="margin: 0;">+<span id="LC1387" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (_tt</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fromChar</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> != _tt</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">toChar</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) {</span></span>
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1388
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<pre style="margin: 0;">+<span id="LC1388" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (model_type == utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">global")) {</span></span>
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1389
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<pre style="margin: 0;">+<span id="LC1389" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> psi_rate = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ApplyNameSpace(psi</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace);</span></span>
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1390
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<pre style="margin: 0;">+<span id="LC1390" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (p</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">model_type</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">psi_term</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = psi_rate;</span></span>
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1391
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<pre style="margin: 0;">+<span id="LC1391" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rate_entry </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= "*" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> psi_rate;</span></span>
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1392
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<pre style="margin: 0;">+<span id="LC1392" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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1393
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<pre style="margin: 0;">+<span id="LC1393" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (p</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">model_type</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">psi_term</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = psi;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1394
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<pre style="margin: 0;">+<span id="LC1394" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rate_entry </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= "*" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> psi;</span></span>
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1395
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<pre style="margin: 0;">+<span id="LC1395" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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1396
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<pre style="margin: 0;">+<span id="LC1396" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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1397
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<pre style="margin: 0;">+<span id="LC1397" 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 (fromChar </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="nf" style="color: #900; font-weight: 600;">-</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;"> toChar </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;"> _tt</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fromChar</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> ")");</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1398
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<pre style="margin: 0;">+<span id="LC1398" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (model_type == utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">global")) {</span></span>
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<pre style="margin: 0;">+<span id="LC1399" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> psi_rate = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ApplyNameSpace(psi_s</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace);</span></span>
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1400
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<pre style="margin: 0;">+<span id="LC1400" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (p</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">model_type</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">psi_s_term</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = psi_rate;</span></span>
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1401
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<pre style="margin: 0;">+<span id="LC1401" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rate_entry </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= "*" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> psi_rate;</span></span>
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1402
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<pre style="margin: 0;">+<span id="LC1402" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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1403
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<pre style="margin: 0;">+<span id="LC1403" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (p</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">model_type</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">psi_s_term</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = psi_s;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1404
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<pre style="margin: 0;">+<span id="LC1404" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rate_entry </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= "*" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> psi_s;</span></span>
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1405
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<pre style="margin: 0;">+<span id="LC1405" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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1406
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<pre style="margin: 0;">+<span id="LC1406" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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1407
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<pre style="margin: 0;">+<span id="LC1407" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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1408
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<pre style="margin: 0;">+<span id="LC1408" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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1409
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<pre style="margin: 0;">+<span id="LC1409" class="line" lang="brainfuck"></span>
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1410
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<pre style="margin: 0;">+<span id="LC1410" class="line" lang="brainfuck"></span>
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1411
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<pre style="margin: 0;">+<span id="LC1411" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> p</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_entry")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = rate_entry;</span></span>
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1412
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<pre style="margin: 0;">+<span id="LC1412" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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1413
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<pre style="margin: 0;">+<span id="LC1413" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return p;</span></span>
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1414
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<pre style="margin: 0;">+<span id="LC1414" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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1415
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<pre style="margin: 0;">+<span id="LC1415" class="line" lang="brainfuck"></span>
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1416
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<pre style="margin: 0;">+<span id="LC1416" 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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1417
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<pre style="margin: 0;">+<span id="LC1417" class="line" lang="brainfuck"></span>
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1418
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<pre style="margin: 0;">+<span id="LC1418" class="line" lang="brainfuck"></span>
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1256
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1419
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<pre style="margin: 0;"> <span id="LC1419" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_GenerateRate (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _tt</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;"> alpha_term</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;"> beta_term</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> omega</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> omega_term) {</span></span>
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<pre style="margin: 0;"> <span id="LC1420" class="line" lang="brainfuck"></span>
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1421
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<pre style="margin: 0;"> <span id="LC1421" 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">@@ -1311,15 +1474,30 @@ lfunction relax.BS_REL._DefineQ (bs_rel, namespace) {</td>
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1474
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<pre style="margin: 0;"> <span id="LC1474" class="line" lang="brainfuck"></span>
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1312
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1475
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<pre style="margin: 0;"> <span id="LC1475" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (component = 1; component </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">= bs_rel</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">components")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">; component </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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1313
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1476
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<pre style="margin: 0;"> <span id="LC1476" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> key = "component_" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> component;</span></span>
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1314
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<pre style="margin: 0;">-<span id="LC1314" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ExecuteCommands ("</span></span>
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1315
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<pre style="margin: 0;">-<span id="LC1315" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> function rate_generator (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model) {</span></span>
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<pre style="margin: 0;">-<span id="LC1316" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_GenerateRate (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">translation_table')</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC1317" class="line" lang="brainfuck"><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;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC1318" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'beta_`component`'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">nonsynonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC1319" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'omega`component`'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">omega_ratio')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component));</span></span>
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<pre style="margin: 0;">-<span id="LC1320" 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="LC1321" 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="LC1322" class="line" lang="brainfuck"></span>
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1477
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<pre style="margin: 0;">+<span id="LC1477" 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="LC1478" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (^'relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">multi_hit' == 'None') {</span></span>
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1479
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<pre style="margin: 0;">+<span id="LC1479" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ExecuteCommands ("</span></span>
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<pre style="margin: 0;">+<span id="LC1480" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> function rate_generator (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model) {</span></span>
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1481
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<pre style="margin: 0;">+<span id="LC1481" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_GenerateRate (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">translation_table')</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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1482
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<pre style="margin: 0;">+<span id="LC1482" class="line" lang="brainfuck"><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;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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1483
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<pre style="margin: 0;">+<span id="LC1483" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'beta_`component`'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">nonsynonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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1484
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<pre style="margin: 0;">+<span id="LC1484" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'omega`component`'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">omega_ratio')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component));</span></span>
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1485
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<pre style="margin: 0;">+<span id="LC1485" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }"</span></span>
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1486
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<pre style="margin: 0;">+<span id="LC1486" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> );</span></span>
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1487
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<pre style="margin: 0;">+<span id="LC1487" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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1488
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<pre style="margin: 0;">+<span id="LC1488" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ExecuteCommands ("</span></span>
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1489
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<pre style="margin: 0;">+<span id="LC1489" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> function rate_generator (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model) {</span></span>
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1490
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<pre style="margin: 0;">+<span id="LC1490" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_GenerateRate</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MH (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">translation_table')</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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1491
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<pre style="margin: 0;">+<span id="LC1491" class="line" lang="brainfuck"><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;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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1492
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<pre style="margin: 0;">+<span id="LC1492" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'beta_`component`'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">nonsynonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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1493
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<pre style="margin: 0;">+<span id="LC1493" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'omega`component`'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">omega_ratio')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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1494
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<pre style="margin: 0;">+<span id="LC1494" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'delta'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">multiple_hit_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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1495
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<pre style="margin: 0;">+<span id="LC1495" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'psi'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">triple_hit_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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1496
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<pre style="margin: 0;">+<span id="LC1496" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'psi'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">triple_hit_rate'));</span></span>
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1497
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<pre style="margin: 0;">+<span id="LC1497" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }"</span></span>
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1498
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<pre style="margin: 0;">+<span id="LC1498" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> );</span></span>
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1499
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<pre style="margin: 0;">+<span id="LC1499" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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1500
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<pre style="margin: 0;">+<span id="LC1500" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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1323
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1501
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<pre style="margin: 0;"> <span id="LC1501" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if ( component </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> bs_rel</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">components")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) {</span></span>
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1324
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1502
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<pre style="margin: 0;"> <span id="LC1502" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddGlobal ( bs_rel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _aux</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">component</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">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;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mixture</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mixture_aux_weight")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component ));</span></span>
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1325
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1503
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<pre style="margin: 0;"> <span id="LC1503" 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 (_aux</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">component</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">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;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">5</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 1);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1334" style="width: 35px; color: rgba(0,0,0,0.3); 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="1512" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1334,6 +1512,7 @@ lfunction relax.BS_REL._DefineQ (bs_rel, namespace) {</td>
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1334
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1512
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<pre style="margin: 0;"> <span id="LC1512" class="line" lang="brainfuck"></span>
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1335
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1513
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<pre style="margin: 0;"> <span id="LC1513" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> bs_rel</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_matrix")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = rate_matrices;</span></span>
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1336
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<td class="new_line diff-line-num" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1514
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<pre style="margin: 0;"> <span id="LC1514" 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(((bs_rel</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">global")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">nucleotideRate("A"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "G")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "1"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "");</span></span>
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1515
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<pre style="margin: 0;">+<span id="LC1515" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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1337
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1516
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<pre style="margin: 0;"> <span id="LC1516" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return bs_rel;</span></span>
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1338
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1517
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<pre style="margin: 0;"> <span id="LC1517" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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1339
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1518
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<pre style="margin: 0;"> <span id="LC1518" 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">@@ -1516,3 +1695,48 @@ lfunction relax._renormalize (v, distro, mean) {</td>
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1516
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1695
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<pre style="margin: 0;"> <span id="LC1695" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return v;</span></span>
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1517
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1696
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<pre style="margin: 0;"> <span id="LC1696" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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1518
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1697
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<pre style="margin: 0;"> <span id="LC1697" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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1698
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<pre style="margin: 0;">+<span id="LC1698" class="line" lang="brainfuck"></span>
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1699
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<pre style="margin: 0;">+<span id="LC1699" 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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1700
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<pre style="margin: 0;">+<span id="LC1700" class="line" lang="brainfuck"></span>
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1701
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<pre style="margin: 0;">+<span id="LC1701" 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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1702
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<pre style="margin: 0;">+<span id="LC1702" class="line" lang="brainfuck"></span>
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1703
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<pre style="margin: 0;">+<span id="LC1703" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report_multi_hit (model_fit</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;"> l1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> l2) {</span></span>
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1704
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<pre style="margin: 0;">+<span id="LC1704" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (^'relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">multi_hit' != "None") {</span></span>
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1705
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<pre style="margin: 0;">+<span id="LC1705" 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(l1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> l2</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;">level rates for multiple</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">hit substitutions\n');</span></span>
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1706
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<pre style="margin: 0;">+<span id="LC1706" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> params = 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;">extract_global_MLE_re (model_fit</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^'terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">multiple_hit_rate');</span></span>
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1707
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<pre style="margin: 0;">+<span id="LC1707" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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1708
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<pre style="margin: 0;">+<span id="LC1708" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> double_rates = {};</span></span>
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1709
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<pre style="margin: 0;">+<span id="LC1709" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (mle; in; params) {</span></span>
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1710
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<pre style="margin: 0;">+<span id="LC1710" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> exp = regexp</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">FindSubexpressions (mle</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;">description'</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">relax\</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">(</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>
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<td class="new_line diff-line-num new" data-linenumber="1711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1711
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<pre style="margin: 0;">+<span id="LC1711" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (None == exp) {</span></span>
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1712
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<pre style="margin: 0;">+<span id="LC1712" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> exp = 'reference';</span></span>
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1713
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<pre style="margin: 0;">+<span id="LC1713" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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1714
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<pre style="margin: 0;">+<span id="LC1714" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> exp = exp</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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1715
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<pre style="margin: 0;">+<span id="LC1715" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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1716
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<pre style="margin: 0;">+<span id="LC1716" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> double_rates </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">exp</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = mle</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^'terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MLE'</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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1717
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<pre style="margin: 0;">+<span id="LC1717" 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(l1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> l2</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> '* 2H rate for **' </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> exp </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> '**: ' </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> Format (double_rates </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">exp</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 8</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 4));</span></span>
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1718
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<pre style="margin: 0;">+<span id="LC1718" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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1719
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<pre style="margin: 0;">+<span id="LC1719" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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1720
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<pre style="margin: 0;">+<span id="LC1720" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1721
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<pre style="margin: 0;">+<span id="LC1721" class="line" lang="brainfuck"><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;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">multiple_hit_rate'</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = double_rates; </span></span>
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1722
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<pre style="margin: 0;">+<span id="LC1722" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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1723
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<pre style="margin: 0;">+<span id="LC1723" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (^'relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">multi_hit' != 'Double') {</span></span>
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1724
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<pre style="margin: 0;">+<span id="LC1724" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> params = 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;">extract_global_MLE_re (model_fit</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^'terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">triple_hit_rate');</span></span>
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1725
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<pre style="margin: 0;">+<span id="LC1725" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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1726
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<pre style="margin: 0;">+<span id="LC1726" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> double_rates = {};</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1727
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<pre style="margin: 0;">+<span id="LC1727" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (mle; in; params) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1728
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<pre style="margin: 0;">+<span id="LC1728" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> exp = regexp</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">FindSubexpressions (mle</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;">description'</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">relax\</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">(</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>
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<td class="new_line diff-line-num new" data-linenumber="1729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1729
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<pre style="margin: 0;">+<span id="LC1729" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (None == exp) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1730
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<pre style="margin: 0;">+<span id="LC1730" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> exp = 'reference';</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1731
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<pre style="margin: 0;">+<span id="LC1731" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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1732
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<pre style="margin: 0;">+<span id="LC1732" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> exp = exp</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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1733
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<pre style="margin: 0;">+<span id="LC1733" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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1734
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<pre style="margin: 0;">+<span id="LC1734" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> double_rates </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">exp</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = mle</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^'terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MLE'</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">+<span id="LC1735" 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(l1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> l2</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> '* 3H rate for **' </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> exp </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> '**: ' </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> Format (double_rates </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">exp</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 8</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 4));</span></span>
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<pre style="margin: 0;">+<span id="LC1736" 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="LC1737" 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="LC1738" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC1739" class="line" lang="brainfuck"><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;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">triple_hit_rate'</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = double_rates; </span></span>
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<pre style="margin: 0;">+<span id="LC1740" 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="LC1741" 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="LC1742" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span></pre>
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<li id="13df3044c13d443b9b6ad8712b47d3bc84725272">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#13df3044c13d443b9b6ad8712b47d3bc84725272"><strong>res/TemplateBatchFiles/SelectionAnalyses/SLAC.bf</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -316,6 +316,8 @@ for (slac.i = 0; slac.i < Abs (slac.filter_specification); slac.i += 1) {</td>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">slac</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MLE </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;">headers : slac</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="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 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;">content : slac</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">results };</span></span>
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">GetString (_hpv</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">HYPHY_VERSION</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="LC320" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">slac</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">runtime</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _hpv;</span></span>
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SpoolJSON (slac</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> slac</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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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<pre style="margin: 0;"> <span id="LC323" 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;">stopTimer (slac</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">timers</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Primary SLAC analysis");</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#43faaf1f56e02d91be5b281472029a32276f7b4c"><strong>res/TemplateBatchFiles/SelectionAnalyses/aBSREL.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">@@ -693,6 +693,10 @@ absrel.json [terms.json.test_results] = {</td>
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<pre style="margin: 0;"> <span id="LC693" class="line" lang="brainfuck"></span>
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694
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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;">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;">stopTimer (absrel</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;"> "Overall");</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;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ToggleEnvVariable ("USE_LAST_RESULTS"</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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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="brainfuck"></span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">GetString (_hpv</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">HYPHY_VERSION</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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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;">absrel</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;">runtime</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _hpv;</span></span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="brainfuck"></span>
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696
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700
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<pre style="margin: 0;"> <span id="LC700" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SpoolJSON (absrel</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;"> absrel</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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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<pre style="margin: 0;"> <span id="LC701" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC702" class="line" lang="brainfuck"></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#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">@@ -556,6 +556,10 @@ fel.json [terms.json.MLE ] = {</td>
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<pre style="margin: 0;"> <span id="LC556" 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;">stopTimer (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">timers</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Total time");</span></span>
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557
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<pre style="margin: 0;"> <span id="LC557" 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;">stopTimer (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">timers</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "FEL analysis");</span></span>
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558
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">GetString (_hpv</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">HYPHY_VERSION</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="LC560" 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;">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;">runtime</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _hpv;</span></span>
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SpoolJSON (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="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;">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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#c259485f7f96dc2ad350d5448508de915c6a9885"><strong>res/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf</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">@@ -292,6 +292,21 @@ function selection.io.report_fit (fit, xp, ss) {</td>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="plaintext">//------------------------------------------------------------------------------</span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext">lfunction selection.io.report_fit_secondary_stats (fit) {</span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext"> p = utility.Array1D (fit[^"terms.branch_length"]);</span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext"> blm = {p,1};</span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext"> for (i,v; in; fit[^"terms.branch_length"]) {</span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext"> BL = 0;</span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext"> for (b,bl; in; v) {</span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext"> BL += bl [^"terms.fit.MLE"];</span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext"> }</span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext"> blm[+i] = Format (BL, 6, 3);</span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext"> }</span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext"> return "" + p + " " + io.SingularOrPlural (p, "partition", "partitions") + ". Total tree length by partition (subs/site) " + Join (", ", blm);</span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext">}</span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext">//------------------------------------------------------------------------------</span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="plaintext">function selection.io.report_lrt (lrt) {</span>
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311
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="plaintext"> return "p-value = " +</span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#c079be28c5231888d711d5c41d1be180223dfce6"><strong>res/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.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">@@ -412,6 +412,10 @@ function doGTR (prefix) {</td>
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<pre style="margin: 0;"> <span id="LC412" 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 (prefix</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "nuc</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;"> "* " </span><span class="nf" style="color: #900; font-weight: 600;">+</span></span>
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413
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 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 (gtr_results</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;"> 3*(^"`prefix`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sample_size")));</span></span>
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReportProgressMessageMD (prefix</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "nuc</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;"> "* " </span><span class="nf" style="color: #900; font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 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_secondary_stats (gtr_results));</span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /* Store nucleotide fit */</span></span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> gtr_rates = utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Map(</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">@@ -435,6 +439,7 @@ function doGTR (prefix) {</td>
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /* Store branch lengths */</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;"> gtr_bls_over_10 = 0;</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;"> gtr_bl_sum = 0;</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></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;"> for (partition_index = 0; partition_index </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> Abs(filter_specification); partition_index </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1) {</span></span>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> selection</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json_store_branch_attribute(json</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue ("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">nucleotide_gtr")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue ("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> display_orders</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">nucleotide_gtr</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -523,6 +528,9 @@ function doPartitionedMG (prefix, keep_lf) {</td>
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="brainfuck"></span>
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529
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="brainfuck"></span>
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530
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReportProgressMessageMD("`prefix`"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "codon</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">fit"</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 (partitioned_mg_results</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;"> (^"`prefix`</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;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue ("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">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="LC531" 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 (prefix</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "nuc</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;"> "* " </span><span class="nf" style="color: #900; font-weight: 600;">+</span></span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 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_secondary_stats (partitioned_mg_results));</span></span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="brainfuck"></span>
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534
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> global_dnds = 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;">extract_global_MLE_re (partitioned_mg_results</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "^" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">omega_ratio"));</span></span>
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535
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<pre style="margin: 0;"> <span id="LC535" 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 (global_dnds</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;"> 'io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReportProgressMessageMD ("`prefix`"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "codon</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">fit"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "* " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> _value_</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">description")</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;"> Format (_value_</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MLE")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">8</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">4));');</span></span>
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="brainfuck"></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#5162429bd3f362a69890c6b040d4be37e11a6308"><strong>res/TemplateBatchFiles/files.lst</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,6 +54,7 @@</td>
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54
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">"RMV","Remove sequences with stop codons from the data.","CleanStopCodons.bf";</span>
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55
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"></span>
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56
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">"","Miscellaneous items.","!Miscellaneous";</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">"DEPS","Analyze Directional Evolution in Protein Sequences (DEPS)","DirectionalREL.bf";</span>
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57
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">"FAA","Fit a multiple fitness class model to amino acid data.","FitnessAAModels.bf";</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">"KH","Perform a Kishino-Hasegawa test on two competing phylogenies","KHTest.bf";</span>
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">"LZ","Compute Lempel-Ziv complexity and entropy of (possibly unaligned) sequences","LZ_Complexity.bf";</span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#c50a9ebb34fca832759d3d11698588f8851c99cb"><strong>res/TemplateBatchFiles/libv3/UtilityFunctions.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">@@ -198,7 +198,9 @@ lfunction utility.MatrixToDict (matrix) {</td>
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> */</span></span>
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">DictToArray (object) {</span></span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> result = {1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">Abs (object)};</span></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ForEachPair(object</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "key"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_value_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "(`&result`)</span><span class="p">[</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">key</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _value_");</span></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (key</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">_value_; in; object) {</span></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> result</span><span class="p">[</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">key</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _value_;</span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return result;</span></span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="brainfuck"></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#5dfec713e3892a936e8b5a63db56c03bee3ec252"><strong>res/TemplateBatchFiles/libv3/all-terms.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">@@ -58,6 +58,7 @@ namespace terms{</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> branch_length = "branch length";</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> alternative = "alternative";</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Null = "null";</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> simulated = "simulated";</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> LRT = "LRT";</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> p_value = "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="LC64" 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">@@ -68,6 +69,7 @@ namespace terms{</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> global_mg94xrev = "Global MG94xREV";</span></span>
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="brainfuck"></span>
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="brainfuck"></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> confidence_interval = "confidence interval";</span></span>
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> lower_bound = "LB";</span></span>
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> upper_bound = "UB";</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> range01 = {</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">@@ -363,6 +365,7 @@ namespace terms{</td>
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363
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365
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> defineQ = "defineQ";</span></span>
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364
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366
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> q_ij = "q_ij";</span></span>
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367
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rate_matrix = "Q";</span></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rate_generator = "rate</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">generator";</span></span>
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366
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> matrix_id = "matrix</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">id";</span></span>
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367
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rate_entry = "rate</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">entry";</span></span>
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371
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> empirical_rates = "empirical</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">rates";</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#94156df91590185798157c724050369c6294262f"><strong>res/TemplateBatchFiles/libv3/models/codon/BS_REL.bf</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,6 +4,8 @@ LoadFunctionLibrary("../parameters.bf");</td>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">LoadFunctionLibrary("</span><span class="nf" style="color: #900; font-weight: 600;">..</span><span class="c1" style="color: #998; font-style: italic;">/frequencies</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bf");</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">LoadFunctionLibrary("</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;">/UtilityFunctions</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bf");</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">LoadFunctionLibrary("MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bf");</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">LoadFunctionLibrary("MG_REV_TRIP</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bf");</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">LoadFunctionLibrary("MG_REV_MH</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bf");</span></span>
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7
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">LoadFunctionLibrary("</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;">/convenience/math</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bf");</span></span>
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8
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/** @module models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span></span>
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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">@@ -415,3 +417,147 @@ function models.codon.BS_REL.get_branch_length(model, tree, node) {</td>
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return bl;</span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @name models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_DefineQ</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MH</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @param {Dict} model</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @param {String} global namespace</span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_DefineQ</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MH (bs_rel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace) {</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="brainfuck"></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;"> rate_matrices = {};</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;"> rg = "function rate_generator (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model) {</span></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV_TRIP</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_GenerateRate_generic (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">translation_table')</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="brainfuck"><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;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'beta_' </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> component</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">nonsynonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component__)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'omega' </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> component</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">omega_ratio')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component__)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'delta'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">multiple_hit_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'psi'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">triple_hit_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</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;"> 'psi_islands'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">triple_hit_rate_syn')</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;"> }";</span></span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (bs_rel</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_generator")</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="LC444" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rg = bs_rel</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_generator")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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445
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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></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="brainfuck"></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;"> bs_rel </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">q_ij")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = &rate_generator;</span></span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> bs_rel </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mixture</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mixture_components")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = {};</span></span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="brainfuck"></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;"> _aux = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GenerateSequentialNames (namespace </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;">bsrel_mixture_aux"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> bs_rel</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">components")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> 1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_");</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _wts = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">helper</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">stick_breaking (_aux</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> None);</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="brainfuck"></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;"> for (component = 1; component </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">= bs_rel</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">components")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">; component </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1) {</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> key = "component_" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> component;</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ExecuteCommands (rg);</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="brainfuck"></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;"> if ( component </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> bs_rel</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">components")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) {</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddGlobal ( bs_rel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _aux</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">component</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">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;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mixture</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mixture_aux_weight")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component ));</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;"> parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">DeclareGlobalWithRanges (_aux</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">component</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">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;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">5</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 1);</span></span>
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<pre style="margin: 0;">+<span id="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;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">DefineQMatrix(bs_rel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace);</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rate_matrices </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">key</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = bs_rel</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_matrix")</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="LC464" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (bs_rel </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^'terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mixture</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mixture_components'</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">key</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _wts </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">component</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> bs_rel</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_matrix")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = rate_matrices;</span></span>
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<pre style="margin: 0;">+<span id="LC468" 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(((bs_rel</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">global")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">nucleotideRate("A"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "G")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "1"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "");</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return bs_rel;</span></span>
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<pre style="margin: 0;">+<span id="LC471" 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="LC473" 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="LC474" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @name models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL_SRV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_DefineQ</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MH</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;"> * @param {Dict} model</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @param {String} global namespace</span></span>
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<pre style="margin: 0;">+<span id="LC477" 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="LC479" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL_SRV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_DefineQ</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MH (bs_rel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace) {</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rate_matrices = {};</span></span>
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<pre style="margin: 0;">+<span id="LC482" 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="LC483" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rg = "function rate_generator (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model) {</span></span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV_TRIP</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_GenerateRate_generic (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">translation_table')</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="brainfuck"><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;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'beta_`component`'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">nonsynonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'omega`component`'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">omega_ratio')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'delta'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">multiple_hit_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'psi'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">triple_hit_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 'psi_islands'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">triple_hit_rate_syn')</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> );</span></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }";</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (bs_rel</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_generator")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) {</span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rg = bs_rel</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_generator")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="brainfuck"></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> bs_rel </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">q_ij")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = &rate_generator;</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> bs_rel </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">time")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = &rate_multiplier;</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="brainfuck"></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> bs_rel </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mixture</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mixture_components")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = {};</span></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ns_components = (bs_rel</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">(utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">components"))</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> syn_components = (bs_rel</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">(utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">components"))</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span 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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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="brainfuck"></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="brainfuck"></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _aux = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GenerateSequentialNames (namespace </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;">bsrel_mixture_aux"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ns_components </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> 1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_");</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _wts = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">helper</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">stick_breaking (_aux</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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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="brainfuck"></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _aux_srv = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GenerateSequentialNames (namespace </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;">bsrel_mixture_aux_srv"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> syn_components </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> 1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_");</span></span>
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _wts_srv = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">helper</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">stick_breaking (_aux_srv</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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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _alphas = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GenerateSequentialNames (namespace </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;">alpha"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> syn_components</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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515
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516
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> mixture = {};</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="brainfuck"></span>
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519
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (s_component = 1; s_component </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">= syn_components; s_component </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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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="brainfuck"></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ExecuteCommands ("</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> function rate_multiplier (option) {</span></span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return {</span></span>
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525
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<pre style="margin: 0;">+<span id="LC525" 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;">global' : {</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> `s_component`) : '`_alphas</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">s_component</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">`'</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" 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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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ^'terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">local' : {</span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ^'terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate' : models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">DNA</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Time (null)</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ^'terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_entry' : '`_alphas</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">s_component</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">`*' </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">DNA</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Time (null)</span></span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> };</span></span>
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<pre style="margin: 0;">+<span id="LC533" 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="LC534" 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="LC535" class="line" lang="brainfuck"></span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (component = 1; component </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">= ns_components; component </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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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> key = "component_" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> s_component </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;"> component;</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ExecuteCommands (rg);</span></span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if ( component </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> ns_components) {</span></span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddGlobal ( bs_rel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _aux</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">component</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">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;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mixture</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mixture_aux_weight")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component ));</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" 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 (_aux</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">component</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">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;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">5</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 1);</span></span>
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<pre style="margin: 0;">+<span id="LC542" 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="LC543" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if ( s_component </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> syn_components) {</span></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddGlobal ( bs_rel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _aux_srv</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">s_component</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mixture</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mixture_aux_weight")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "SRV " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> s_component ));</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">DeclareGlobalWithRanges (_aux_srv</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">s_component</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">5</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 1);</span></span>
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<pre style="margin: 0;">+<span id="LC546" 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="LC547" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">DefineQMatrix(bs_rel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace);</span></span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> rate_matrices </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">key</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = bs_rel</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_matrix")</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="LC549" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (bs_rel </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^'terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mixture</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mixture_components'</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">key</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AppendMultiplicativeTerm (_wts </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">component</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">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;"> _wts_srv</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">s_component</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> 1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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<pre style="margin: 0;">+<span id="LC550" 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="LC551" 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="LC552" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> __rp = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ConstrainMeanOfSet (_alphas</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _wts_srv</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;"> namespace);</span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">DeclareGlobal (__rp</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="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> null);</span></span>
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<pre style="margin: 0;">+<span id="LC556" 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;">helper</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">copy_definitions (bs_rel</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^'terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters'</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> __rp);</span></span>
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> bs_rel</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_matrix")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = rate_matrices;</span></span>
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<pre style="margin: 0;">+<span id="LC560" 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(((bs_rel</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">global")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">nucleotideRate("A"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "G")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "1"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "");</span></span>
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return bs_rel;</span></span>
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#c7933e171033f4eac9d83419583cca5474f9266c"><strong>res/TemplateBatchFiles/libv3/tasks/estimators.bf</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -754,7 +754,7 @@ lfunction estimators.FitLF(data_filter, tree, model_map, initial_values, model_o</td>
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<pre style="margin: 0;"> <span id="LC754" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC755" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> lf_id = &likelihoodFunction;</span></span>
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<pre style="margin: 0;"> <span id="LC756" 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;">ExecuteInGlobalNamespace ("LikelihoodFunction `lf_id` = (`&lf_components`)");</span></span>
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<pre style="margin: 0;">-<span id="LC757" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC757" 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="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;"> df = 0;</span></span>
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<pre style="margin: 0;"> <span id="LC760" 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">@@ -122,7 +122,7 @@ namespace hy_global {</td>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">kErrorStringDatasetRefIndexError</span> <span class="p">(</span><span class="s" style="color: #d14;">"Dataset index reference out of range"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">kErrorStringMatrixExportError</span> <span class="p">(</span><span class="s" style="color: #d14;">"Export matrix called with a non-polynomial matrix argument"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">kErrorStringNullOperand</span> <span class="p">(</span><span class="s" style="color: #d14;">"Attempting to operate on an undefined value; this is probably the result of an earlier 'soft' error condition"</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">kHyPhyVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"2.5.3<span class="idiff left right">1</span>"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">kHyPhyVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"2.5.3<span class="idiff left right">2</span>"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">kNoneToken</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"None"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">kNullToken</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"null"</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#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">@@ -202,6 +202,8 @@ public:</td>
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">virtual</span></span>
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203
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cpp"> <span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Optimize</span> <span class="p">(</span><span class="n" style="color: #333;">_AssociativeList</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">options</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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204
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="cpp"> <span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ConstructCategoryMatrix</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">_SimpleList</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nil</span><span class="p">);</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">_String</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"> <span class="n" style="color: #333;">GetMyName</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">SimplexMethod</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;">precision</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;">max_iterations</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100000UL</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;">max_evals</span> <span class="o" style="font-weight: 600;">=</span> <span class="mh" style="color: #099;">0xFFFFFF</span><span class="p">);</span></span>
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Anneal</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;">precision</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#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">@@ -793,7 +793,7 @@ void _LikelihoodFunction::Rebuild (bool rescan_parameters) {</td>
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<pre style="margin: 0;"> <span id="LC793" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC794" class="line" lang="cpp"> <span class="p">}</span></span>
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795
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<pre style="margin: 0;"> <span id="LC795" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">catch</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;">code</span><span class="p">)</span> <span class="p">{</span></span>
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796
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<pre style="margin: 0;">-<span id="LC796" class="line" lang="cpp"> <span class="n" style="color: #333;">ReportWarning</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"Likelihood function cleared because partition index '"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span> <span class="n" style="color: #333;">code</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"' points to invalid components<span class="idiff left right">"</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="cpp"> <span class="n" style="color: #333;">ReportWarning</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"Likelihood function <span class="idiff left">"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">GetMyName</span></span><span class="p"><span class="idiff">().</span></span><span class="n" style="color: #333;"><span class="idiff">Enquote</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_String</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" </span>cleared because partition index '"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span> <span class="n" style="color: #333;">code</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"' points to invalid components<span class="idiff">. "</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ignored_error</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC797" class="line" lang="cpp"> <span class="n" style="color: #333;">Clear</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC798" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC799" 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">@@ -1524,7 +1524,15 @@ void _LikelihoodFunction::MPI_LF_Compute (long, bool)</td>
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<pre style="margin: 0;"> <span id="LC1524" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1526" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1527" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC1527" 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="LC1528" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">_String</span> <span class="n" style="color: #333;">_LikelihoodFunction</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetMyName</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1529" 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="n" style="color: #333;">hyphy_global_objects</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FindLikeFuncIndex</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="k" style="font-weight: 600;">this</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1530" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">0</span><span class="p">)</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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kEmptyString</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1532" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1533" 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;">hyphy_global_objects</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetObjectNameByType</span> <span class="p">(</span><span class="n" style="color: #333;">HY_BL_LIKELIHOOD_FUNCTION</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1534" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1535" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC1536" 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="LC1537" class="line" lang="cpp"><span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_LikelihoodFunction</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ConstructCategoryMatrix</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">_SimpleList</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">whichParts</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">runMode</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">remap</span><span class="p">,</span> <span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">storageID</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1538" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">hDim</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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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#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">@@ -2028,6 +2028,7 @@ bool _Matrix::IsValidTransitionMatrix() const {</td>
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<pre style="margin: 0;"> <span id="LC2028" class="line" lang="cpp"> <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;">0L</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2029" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">tolerance</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kMachineEpsilon</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">10.</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2030" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">d</span><span class="p">;</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC2031" class="line" lang="cpp"> <span class="n" style="color: #333;">sums</span> <span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2032" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">d</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC2033" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">term</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;">idx</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC2034" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">term</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">term</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">1.0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7628,11 +7629,11 @@ void _Matrix::RecursiveIndexSort (long from, long to, _SimpleList* index) {</td>
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<pre style="margin: 0;"> <span id="LC7629" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC7630" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC7631" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC7631" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bottommove</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">CompareRows</span> <span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bottommove</span><span class="p">,</span> <span class="n" style="color: #333;">middle</span><span class="p">)</span> <span class="o" style="font-weight: 600;">><span class="idiff left right">=</span></span> <span class="mi" style="color: #099;">0L</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC7632" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bottommove</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">CompareRows</span> <span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bottommove</span><span class="p">,</span> <span class="n" style="color: #333;">middle</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0L</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC7633" class="line" lang="cpp"> <span class="n" style="color: #333;">bottommove</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC7634" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC7635" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">from</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">to</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC7635" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">topmove</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">to</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">CompareRows</span> <span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">topmove</span><span class="p">,</span><span class="n" style="color: #333;">middle</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<span class="idiff left right">=</span></span> <span class="mi" style="color: #099;">0L</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC7636" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">topmove</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">to</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">CompareRows</span> <span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">topmove</span><span class="p">,</span><span class="n" style="color: #333;">middle</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0L</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC7637" class="line" lang="cpp"> <span class="n" style="color: #333;">topmove</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC7638" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC7639" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7642,7 +7643,7 @@ void _Matrix::RecursiveIndexSort (long from, long to, _SimpleList* index) {</td>
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<pre style="margin: 0;"> <span id="LC7643" class="line" lang="cpp"> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Swap</span><span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bottommove</span><span class="p">,</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC7644" class="line" lang="cpp"> <span class="n" style="color: #333;">bottommove</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC7645" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC7645" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bottommove</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">CompareRows</span> <span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bottommove</span><span class="p">,</span> <span class="n" style="color: #333;">middle</span><span class="p">)</span> <span class="o" style="font-weight: 600;">><span class="idiff left right">=</span></span> <span class="mi" style="color: #099;">0L</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC7646" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bottommove</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">CompareRows</span> <span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bottommove</span><span class="p">,</span> <span class="n" style="color: #333;">middle</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0L</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC7647" class="line" lang="cpp"> <span class="n" style="color: #333;">bottommove</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC7648" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC7649" 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">@@ -7654,7 +7655,7 @@ void _Matrix::RecursiveIndexSort (long from, long to, _SimpleList* index) {</td>
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<pre style="margin: 0;"> <span id="LC7655" class="line" lang="cpp"> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Swap</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">topmove</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC7656" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC7657" class="line" lang="cpp"> <span class="n" style="color: #333;">topmove</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC7657" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">topmove</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">to</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">CompareRows</span> <span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">topmove</span><span class="p">,</span><span class="n" style="color: #333;">middle</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<span class="idiff left right">=</span></span> <span class="mi" style="color: #099;">0L</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC7658" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">topmove</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">to</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">CompareRows</span> <span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">topmove</span><span class="p">,</span><span class="n" style="color: #333;">middle</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0L</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC7659" class="line" lang="cpp"> <span class="n" style="color: #333;">topmove</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC7660" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC7661" 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">@@ -7760,6 +7761,13 @@ HBLObjectRef _Matrix::SortMatrixOnColumn (HBLObjectRef mp, HBLObjectRef ca</td>
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<pre style="margin: 0;"> <span id="LC7761" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC7762" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC7763" class="line" lang="cpp"> <span class="n" style="color: #333;">theColumn</span><span class="p">.</span><span class="n" style="color: #333;">RecursiveIndexSort</span> <span class="p">(</span><span class="mi" style="color: #099;">0</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;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">idx</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC7764" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*for (long i = 1; i < hDim; i++) {</span></span>
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<pre style="margin: 0;">+<span id="LC7765" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (theColumn.theData[i-1] > theColumn.theData[i]) {</span></span>
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7766
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<pre style="margin: 0;">+<span id="LC7766" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> HandleApplicationError("Resulting matrix is not properly sorted");</span></span>
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<pre style="margin: 0;">+<span id="LC7767" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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7768
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<pre style="margin: 0;">+<span id="LC7768" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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<pre style="margin: 0;">+<span id="LC7769" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC7770" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC7771" class="line" lang="cpp"> <span class="n" style="color: #333;">_Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_returnMatrixOrUseCache</span><span class="p">(</span><span class="n" style="color: #333;">hDim</span><span class="p">,</span> <span class="n" style="color: #333;">vDim</span><span class="p">,</span> <span class="n" style="color: #333;">_NUMERICAL_TYPE</span><span class="p">,</span> <span class="n" style="color: #333;">theIndex</span><span class="p">,</span> <span class="n" style="color: #333;">cache</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC7772" class="line" lang="cpp"></span>
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7773
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<pre style="margin: 0;"> <span id="LC7773" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">theIndex</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#d5409d207f9902b4fd1c68a0af284b4294fed610"><strong>src/core/simplelist.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">@@ -1327,12 +1327,12 @@ void _SimpleList::RecursiveIndexSort (long from, long to, _SimpleList* index) {</td>
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<pre style="margin: 0;"> <span id="LC1327" class="line" lang="cpp"> <span class="n" style="color: #333;">bottommove</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;">topmove</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;">temp</span><span class="p">,</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">imiddleV</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;">index</span><span class="p">)(</span><span class="n" style="color: #333;">middle</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1328" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1329" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1330" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bottommove</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">from</span><span class="p">)</span><span class="o" style="font-weight: 600;">&&</span><span class="p">(</span><span class="n" style="color: #333;">Compare</span><span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bottommove</span><span class="p">,</span><span class="n" style="color: #333;">middle</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><span class="idiff left">!</span>=</span> <span class="n" style="color: #333;">kCompare<span class="idiff right">Less</span></span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1330" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bottommove</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">from</span><span class="p">)</span><span class="o" style="font-weight: 600;">&&</span><span class="p">(</span><span class="n" style="color: #333;">Compare</span><span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bottommove</span><span class="p">,</span><span class="n" style="color: #333;">middle</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><span class="idiff left">=</span>=</span> <span class="n" style="color: #333;">kCompare<span class="idiff right">Greater</span></span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1331" class="line" lang="cpp"> <span class="n" style="color: #333;">bottommove</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1332" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1333" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1334" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">from</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">to</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1335" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">topmove</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">to</span><span class="p">)</span><span class="o" style="font-weight: 600;">&&</span><span class="p">(</span><span class="n" style="color: #333;">Compare</span><span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">topmove</span><span class="p">,</span><span class="n" style="color: #333;">middle</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><span class="idiff left">!</span>=</span> <span class="n" style="color: #333;">kCompare<span class="idiff right">Greater</span></span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1335" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">topmove</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">to</span><span class="p">)</span><span class="o" style="font-weight: 600;">&&</span><span class="p">(</span><span class="n" style="color: #333;">Compare</span><span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">topmove</span><span class="p">,</span><span class="n" style="color: #333;">middle</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><span class="idiff left">=</span>=</span> <span class="n" style="color: #333;">kCompare<span class="idiff right">Less</span></span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1336" class="line" lang="cpp"> <span class="n" style="color: #333;">topmove</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1337" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1338" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1342" style="width: 35px; color: rgba(0,0,0,0.3); 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="1342" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1342,7 +1342,7 @@ void _SimpleList::RecursiveIndexSort (long from, long to, _SimpleList* index) {</td>
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<pre style="margin: 0;"> <span id="LC1342" class="line" lang="cpp"> <span class="n" style="color: #333;">Exchange</span> <span class="p">(</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bottommove</span><span class="p">],</span> <span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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1343
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<pre style="margin: 0;"> <span id="LC1343" class="line" lang="cpp"> <span class="n" style="color: #333;">Exchange</span> <span class="p">(</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bottommove</span><span class="p">],</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC1344" class="line" lang="cpp"> <span class="n" style="color: #333;">bottommove</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1345" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bottommove</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">from</span><span class="p">)</span><span class="o" style="font-weight: 600;">&&</span><span class="p">(</span><span class="n" style="color: #333;">Compare</span><span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bottommove</span><span class="p">,</span><span class="n" style="color: #333;">middle</span><span class="p">)</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span>=</span> <span class="n" style="color: #333;">kCompare<span class="idiff right">Less</span></span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1345" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bottommove</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">from</span><span class="p">)</span><span class="o" style="font-weight: 600;">&&</span><span class="p">(</span><span class="n" style="color: #333;">Compare</span><span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bottommove</span><span class="p">,</span><span class="n" style="color: #333;">middle</span><span class="p">)</span><span class="o" style="font-weight: 600;"><span class="idiff left">=</span>=</span> <span class="n" style="color: #333;">kCompare<span class="idiff right">Greater</span></span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1346" class="line" lang="cpp"> <span class="n" style="color: #333;">bottommove</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1347" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1348" 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">@@ -1353,7 +1353,7 @@ void _SimpleList::RecursiveIndexSort (long from, long to, _SimpleList* index) {</td>
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1353
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<pre style="margin: 0;"> <span id="LC1353" class="line" lang="cpp"> <span class="n" style="color: #333;">Exchange</span> <span class="p">(</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">topmove</span><span class="p">],</span> <span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC1354" class="line" lang="cpp"> <span class="n" style="color: #333;">Exchange</span> <span class="p">(</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">topmove</span><span class="p">],</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC1355" class="line" lang="cpp"> <span class="n" style="color: #333;">topmove</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1356" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">topmove</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">to</span><span class="p">)</span><span class="o" style="font-weight: 600;">&&</span><span class="p">(</span><span class="n" style="color: #333;">Compare</span><span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">topmove</span><span class="p">,</span><span class="n" style="color: #333;">middle</span><span class="p">)</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span>=</span> <span class="n" style="color: #333;">kCompare<span class="idiff right">Greater</span></span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1356" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">topmove</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">to</span><span class="p">)</span><span class="o" style="font-weight: 600;">&&</span><span class="p">(</span><span class="n" style="color: #333;">Compare</span><span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">topmove</span><span class="p">,</span><span class="n" style="color: #333;">middle</span><span class="p">)</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span>=</span> <span class="n" style="color: #333;">kCompare<span class="idiff right">Less</span></span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1357" class="line" lang="cpp"> <span class="n" style="color: #333;">topmove</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1358" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1359" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#3db5a40160a9b0d2ceac81e7037e883bdd54b8f7"><strong>src/core/topology.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">@@ -1346,7 +1346,7 @@ HBLObjectRef _TreeTopology::MaximumParsimony (HBLObjectRef parameters,HBLObjectR</td>
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<pre style="margin: 0;"> <span id="LC1346" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC1347" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC1348" 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;">iterator</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_leaf</span> <span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// labeled node</span></span>
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<pre style="margin: 0;">-<span id="LC1349" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">my_label</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1349" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">my_label</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0L</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1350" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">best_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.e100</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1351" 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;">iterator</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">parent</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">has_labels</span><span class="p">.</span><span class="n" style="color: #333;">get</span> <span class="p">(</span><span class="n" style="color: #333;">iterator</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">in_object</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1352" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// either a root or not a part of the labeled tree</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d482898df35710ff14413712f36f8cac7cd945b5#aeaccdf9a873c05871ba3cd1bca1ae0e9f8254e4"><strong>src/mains/unix.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -80,8 +80,6 @@ const char hy_help_message [] =</td>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"><span class="s" style="color: #d14;">" -c calculator mode; causes HyPhy to drop into an expression evaluation until 'exit' is typed</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"><span class="s" style="color: #d14;">" -d debug mode; causes HyPhy to drop into an expression evaluation mode upon script error</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"><span class="s" style="color: #d14;">" -i interactive mode; causes HyPhy to always prompt the user for analysis options, even when defaults are available</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cpp"><span class="s" style="color: #d14;">" -p postprocessor mode; drops HyPhy into an interactive mode where general post-processing scripts can be selected</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="cpp"><span class="s" style="color: #d14;">" upon analysis completion</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"><span class="s" style="color: #d14;">" -m write diagnostic messages to messages.log</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"><span class="s" style="color: #d14;">"optional global arguments:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"><span class="s" style="color: #d14;">" BASEPATH=directory path defines the base directory for all path operations (default is pwd)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</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">@@ -179,7 +177,6 @@ void ReadInTemplateFiles (void);</td>
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">DisplayListOfChoices</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="LC178" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessConfigStr</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span><span class="p">);</span></span>
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessKWStr</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">arg</span><span class="p">,</span> <span class="n" style="color: #333;">_String</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">arg2</span><span class="p">,</span> <span class="n" style="color: #333;">_AssociativeList</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kwargs</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ReadInPostFiles</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="LC180" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">DisplayListOfPostChoices</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="LC181" class="line" lang="cpp"><span class="n" style="color: #333;">_String</span> <span class="nf" style="color: #900; font-weight: 600;">getLibraryPath</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="LC182" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -187,8 +184,7 @@ _String getLibraryPath (void);</td>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">usePostProcessors</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="LC191" class="line" lang="cpp"> <span class="n" style="color: #333;">calculatorMode</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="LC187" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">calculatorMode</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="LC188" class="line" lang="cpp"> <span class="n" style="color: #333;">updateMode</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="LC189" class="line" lang="cpp"> <span class="n" style="color: #333;">pipeMode</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="LC190" class="line" lang="cpp"> <span class="n" style="color: #333;">logInputMode</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -344,69 +340,6 @@ void ReadInTemplateFiles(void) {</td>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="cpp"><span class="p">}</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="LC347" 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="LC348" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ReadInPostFiles</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="LC349" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">_String</span> <span class="n" style="color: #333;">kSeparator</span> <span class="p">(</span><span class="s" style="color: #d14;">"SEPARATOR"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (!likeFuncList.lLength)</span></span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// return;</span></span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="cpp"> <span class="n" style="color: #333;">_String</span> <span class="n" style="color: #333;">dir_sep</span> <span class="p">(</span><span class="n" style="color: #333;">get_platform_directory_char</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="cpp"> <span class="n" style="color: #333;">_String</span> <span class="n" style="color: #333;">fileIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libArgDir</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">hy_standard_library_directory</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">dir_sep</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"postprocessors.lst"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">modelList</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span> <span class="p">(</span><span class="n" style="color: #333;">fileIndex</span><span class="p">.</span><span class="n" style="color: #333;">get_str</span><span class="p">(),</span><span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC358" 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;">modelList</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="cpp"> <span class="n" style="color: #333;">_String</span> <span class="n" style="color: #333;">theData</span> <span class="p">(</span><span class="n" style="color: #333;">modelList</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span> <span class="p">(</span><span class="n" style="color: #333;">modelList</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC365" 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;">length</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="cpp"> <span class="n" style="color: #333;">_ElementaryCommand</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ExtractConditions</span><span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">availablePostProcessors</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC368" 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;">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;">availablePostProcessors</span><span class="p">.</span><span class="n" style="color: #333;">countitems</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="cpp"> <span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">thisString</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">availablePostProcessors</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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370
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="cpp"> <span class="n" style="color: #333;">_List</span> <span class="n" style="color: #333;">thisFile</span><span class="p">;</span></span>
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371
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="cpp"> <span class="n" style="color: #333;">_ElementaryCommand</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ExtractConditions</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">thisString</span><span class="p">,</span><span class="n" style="color: #333;">thisString</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">FirstNonSpaceIndex</span><span class="p">(),</span><span class="n" style="color: #333;">thisFile</span><span class="p">,</span><span class="sc" style="color: #d14;">','</span><span class="p">);</span></span>
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372
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">thisFile</span><span class="p">.</span><span class="n" style="color: #333;">lLength</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
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373
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="cpp"> <span class="n" style="color: #333;">availablePostProcessors</span><span class="p">.</span><span class="n" style="color: #333;">Delete</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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374
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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375
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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376
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="cpp"> <span class="p">}</span></span>
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377
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<pre style="margin: 0;">-<span id="LC377" 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="mi" style="color: #099;">3</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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378
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="cpp"> <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;">thisFile</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">))</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">StripQuotes</span><span class="p">();</span></span>
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379
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="cpp"> <span class="p">}</span></span>
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380
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><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;">thisFile</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;">kSeparator</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
381
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="cpp"> <span class="n" style="color: #333;">fileIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">((</span><span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">pathNames</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;">hy_standard_library_directory</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">dir_sep</span> <span class="o" style="font-weight: 600;">&</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">thisFile</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dummyFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span> <span class="p">(</span><span class="n" style="color: #333;">fileIndex</span><span class="p">,</span><span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>
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383
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<pre style="margin: 0;">-<span id="LC383" 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;">dummyFile</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
384
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="cpp"> <span class="n" style="color: #333;">fileIndex</span> <span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">libArgDir</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">hy_standard_library_directory</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">dir_sep</span> <span class="o" style="font-weight: 600;">&</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">thisFile</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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385
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<td class="new_line diff-line-num old" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC385" class="line" lang="cpp"> <span class="n" style="color: #333;">dummyFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span> <span class="p">(</span><span class="n" style="color: #333;">fileIndex</span><span class="p">,</span><span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
386
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dummyFile</span><span class="p">)</span> <span class="p">{</span></span>
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388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span> <span class="p">(</span><span class="n" style="color: #333;">dummyFile</span><span class="p">);</span></span>
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389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="cpp"> <span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">condition</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">thisFile</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">condition</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nonempty</span><span class="p">())</span> <span class="p">{</span></span>
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391
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="cpp"> <span class="n" style="color: #333;">_Formula</span> <span class="n" style="color: #333;">condCheck</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">condition</span><span class="p">,</span><span class="n" style="color: #333;">nil</span><span class="p">);</span></span>
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392
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="cpp"> <span class="n" style="color: #333;">HBLObjectRef</span> <span class="n" style="color: #333;">condCheckRes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">condCheck</span><span class="p">.</span><span class="n" style="color: #333;">Compute</span><span class="p">();</span></span>
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393
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<pre style="margin: 0;">-<span id="LC393" 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;">condCheckRes</span><span class="p">)</span><span class="o" style="font-weight: 600;">||</span><span class="p">(</span><span class="n" style="color: #333;">condCheckRes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Value</span><span class="p">()</span><span class="o" style="font-weight: 600;"><</span><span class="mf" style="color: #099;">.5</span><span class="p">))</span> <span class="p">{</span></span>
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394
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="cpp"> <span class="n" style="color: #333;">availablePostProcessors</span><span class="p">.</span><span class="n" style="color: #333;">Delete</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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395
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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396
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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397
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="cpp"> <span class="p">}</span></span>
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398
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="cpp"> <span class="p">}</span></span>
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399
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">thisFile</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;">fileIndex</span><span class="p">;</span></span>
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400
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<td class="new_line diff-line-num old" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC400" class="line" lang="cpp"> <span class="n" style="color: #333;">availablePostProcessors</span><span class="p">.</span><span class="n" style="color: #333;">Replace</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;">thisFile</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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401
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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402
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="cpp"> <span class="p">}</span></span>
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403
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="cpp"> <span class="p">}</span></span>
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404
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="cpp"> <span class="n" style="color: #333;">availablePostProcessors</span><span class="p">.</span><span class="n" style="color: #333;">Delete</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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405
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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406
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="cpp"> <span class="p">}</span></span>
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407
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="cpp"></span>
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408
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp"></span>
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344
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//__________________________________________________________________________________</span></span>
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345
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">DisplayListOfChoices</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -579,12 +512,7 @@ void ProcessConfigStr (_String const & conf) {</td>
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579
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512
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="cpp"> <span class="p">}</span></span>
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580
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513
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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514
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC582" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'p'</span><span class="p">:</span></span>
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583
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'P'</span><span class="p">:</span> <span class="p">{</span></span>
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584
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="cpp"> <span class="n" style="color: #333;">usePostProcessors</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC585" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC586" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC587" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'c'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'c'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC516" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'C'</span><span class="p">:</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC517" class="line" lang="cpp"> <span class="n" style="color: #333;">calculatorMode</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</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">@@ -1026,39 +954,7 @@ int main (int argc, char* argv[]) {</td>
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1026
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954
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<pre style="margin: 0;"> <span id="LC954" class="line" lang="cpp"> <span class="n" style="color: #333;">ex</span><span class="p">.</span><span class="n" style="color: #333;">Execute</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC955" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC956" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC1029" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">usePostProcessors</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;">updateMode</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1030" class="line" lang="cpp"> <span class="n" style="color: #333;">ReadInPostFiles</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC1031" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span> <span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">**********Continue with result processing (y/n)?"</span><span class="p">);</span></span>
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1032
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<td class="new_line diff-line-num old" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1032" class="line" lang="cpp"> <span class="n" style="color: #333;">_String</span> <span class="n" style="color: #333;">c_str</span> <span class="p">(</span><span class="n" style="color: #333;">StringFromConsole</span><span class="p">());</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1033
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<td class="new_line diff-line-num old" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1033" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1034
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<td class="new_line diff-line-num old" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1034" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">logInputMode</span><span class="p">)</span> <span class="p">{</span></span>
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1035
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<td class="new_line diff-line-num old" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1035" class="line" lang="cpp"> <span class="n" style="color: #333;">loggedUserInputs</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">c_str</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1036
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<pre style="margin: 0;">-<span id="LC1036" class="line" lang="cpp"> <span class="p">}</span></span>
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1037
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<td class="new_line diff-line-num old" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1037" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="1038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1038
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<pre style="margin: 0;">-<span id="LC1038" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c_str</span><span class="p">.</span><span class="n" style="color: #333;">get_char</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="sc" style="color: #d14;">'n'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">c_str</span><span class="p">.</span><span class="n" style="color: #333;">get_char</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="sc" style="color: #d14;">'N'</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1039
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<td class="new_line diff-line-num old" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1039" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">choice</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DisplayListOfPostChoices</span><span class="p">();</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1040
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<pre style="margin: 0;">-<span id="LC1040" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">choice</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1041
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<pre style="margin: 0;">-<span id="LC1041" class="line" lang="cpp"> <span class="n" style="color: #333;">_ExecutionList</span> <span class="n" style="color: #333;">postEx</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1042
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<pre style="margin: 0;">-<span id="LC1042" class="line" lang="cpp"> <span class="n" style="color: #333;">argFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">_List</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">availablePostProcessors</span><span class="p">(</span><span class="n" style="color: #333;">choice</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">))(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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1043
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<pre style="margin: 0;">-<span id="LC1043" class="line" lang="cpp"> <span class="n" style="color: #333;">PushFilePath</span> <span class="p">(</span><span class="n" style="color: #333;">argFile</span><span class="p">);</span></span>
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1044
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<pre style="margin: 0;">-<span id="LC1044" class="line" lang="cpp"> <span class="n" style="color: #333;">ReadBatchFile</span> <span class="p">(</span><span class="n" style="color: #333;">argFile</span><span class="p">,</span> <span class="n" style="color: #333;">postEx</span><span class="p">);</span></span>
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1045
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<td class="new_line diff-line-num old" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1045" class="line" lang="cpp"> <span class="n" style="color: #333;">postEx</span><span class="p">.</span><span class="n" style="color: #333;">Execute</span><span class="p">();</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1046
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<td class="new_line diff-line-num old" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1046" class="line" lang="cpp"> <span class="n" style="color: #333;">PopFilePath</span> <span class="p">();</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1047
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<pre style="margin: 0;">-<span id="LC1047" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span> <span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">**********Continue with result processing (y/n)?"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1048
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<td class="new_line diff-line-num old" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1048" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1049
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<td class="new_line diff-line-num old" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1049" class="line" lang="cpp"> <span class="n" style="color: #333;">c_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringFromConsole</span><span class="p">();</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1050
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<td class="new_line diff-line-num old" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1050" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">logInputMode</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1051
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<td class="new_line diff-line-num old" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1051" class="line" lang="cpp"> <span class="n" style="color: #333;">loggedUserInputs</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">c_str</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1052
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<td class="new_line diff-line-num old" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1052" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num old" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1053" class="line" lang="cpp"></span>
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1054
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<td class="new_line diff-line-num old" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1054" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c_str</span><span class="p">.</span><span class="n" style="color: #333;">get_char</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="sc" style="color: #d14;">'n'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">c_str</span><span class="p">.</span><span class="n" style="color: #333;">get_char</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="sc" style="color: #d14;">'N'</span> <span class="p">)</span> <span class="p">{</span></span>
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1055
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<td class="new_line diff-line-num old" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1055" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1056
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<td class="new_line diff-line-num old" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1056" class="line" lang="cpp"> <span class="p">}</span></span>
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1057
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<pre style="margin: 0;">-<span id="LC1057" class="line" lang="cpp"></span>
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1058
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<pre style="margin: 0;">-<span id="LC1058" class="line" lang="cpp"> <span class="n" style="color: #333;">choice</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DisplayListOfPostChoices</span><span class="p">();</span></span>
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1059
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<pre style="margin: 0;">-<span id="LC1059" class="line" lang="cpp"> <span class="p">}</span></span>
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1060
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<pre style="margin: 0;">-<span id="LC1060" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1061" class="line" lang="cpp"> <span class="p">}</span></span>
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957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="cpp"> </span>
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1062
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958
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<pre style="margin: 0;"> <span id="LC958" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __HYPHYMPI__</span></span>
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1063
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959
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<pre style="margin: 0;"> <span id="LC959" class="line" lang="cpp"> <span class="p">}</span></span>
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1064
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960
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<pre style="margin: 0;"> <span id="LC960" class="line" lang="cpp"> <span class="n" style="color: #333;">ReportWarning</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"Node "</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">rank</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">" is shutting down</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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