<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN" "http://www.w3.org/TR/REC-html40/loose.dtd">
<html lang="en" style='--code-editor-font: var(--default-mono-font, "GitLab Mono"), JetBrains Mono, Menlo, DejaVu Sans Mono, Liberation Mono, Consolas, Ubuntu Mono, Courier New, andale mono, lucida console, monospace;'>
<head>
<meta content="text/html; charset=US-ASCII" http-equiv="Content-Type">
<title>
GitLab
</title>
<style data-premailer="ignore" type="text/css">
a { color: #1068bf; }
</style>
<style>img {
max-width: 100%; height: auto;
}
body {
font-size: .875rem;
}
body {
-webkit-text-shadow: rgba(255,255,255,.01) 0 0 1px;
}
body {
font-family: "GitLab Sans",-apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,"Noto Sans",Ubuntu,Cantarell,"Helvetica Neue",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji"; font-size: inherit;
}
</style>
</head>
<body style='font-size: inherit; -webkit-text-shadow: rgba(255,255,255,.01) 0 0 1px; font-family: "GitLab Sans",-apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,"Noto Sans",Ubuntu,Cantarell,"Helvetica Neue",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji";'>
<div class="content">
<h3 style="margin-top: 20px; margin-bottom: 10px;">
Étienne Mollier pushed to branch upstream at <a href="https://salsa.debian.org/med-team/hyphy">Debian Med / hyphy</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
</h4>
<ul>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/hyphy/-/commit/65547ade91167ae6589a244327500e8e1a4cf100">65547ade</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-11-03T11:30:59+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 2.5.63+dfsg</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
13 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#c772592437fe6a7d4e11445521dd00b76827f448">
res/TemplateBatchFiles/CleanStopCodons.bf
</a>
</li>
<li class="file-stats">
<a href="#bc98d7300147ce39ef8ee0f9b35f3252bebd01d2">
res/TemplateBatchFiles/SelectionAnalyses/MEME.bf
</a>
</li>
<li class="file-stats">
<a href="#80cb7c212661a2afbd05c16dce9f84f45709578e">
res/TemplateBatchFiles/SelectionAnalyses/PRIME.bf
</a>
</li>
<li class="file-stats">
<a href="#02cbcb76e8ce1aa3e72d55e6696cda20813d57b6">
src/core/batchlan.cpp
</a>
</li>
<li class="file-stats">
<a href="#cbedcf5fec686e5f563504b995c5d7d07fd8c6b2">
src/core/batchlanruntime.cpp
</a>
</li>
<li class="file-stats">
<a href="#d09b45303442d6299978fa8d0c8f3338d6a17886">
src/core/formula.cpp
</a>
</li>
<li class="file-stats">
<a href="#07aceb8d215a75908cea626d9c80bc2a7c06639c">
src/core/global_things.cpp
</a>
</li>
<li class="file-stats">
<a href="#46380d67c22541ee76ad7fa2f39c30110df90a7c">
src/core/include/batchlan.h
</a>
</li>
<li class="file-stats">
<a href="#40fc4f1e42852e6f2302e213cd9b3646abe98291">
src/core/include/formula.h
</a>
</li>
<li class="file-stats">
<a href="#7277ab70f1a79733638d6141d1cb1d3f8b9c26c2">
src/core/include/likefunc.h
</a>
</li>
<li class="file-stats">
<a href="#2a8dd324ded753b0b3c559ac3950a2881ccd7a93">
src/core/likefunc.cpp
</a>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Changes:
</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/65547ade91167ae6589a244327500e8e1a4cf100#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong style="font-weight: 600;">CMakeLists.txt</strong></a>
<hr style="overflow: hidden; border: 1px solid #e1e1e1;">
<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#ffffff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="236" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="236" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -236,7 +236,7 @@ if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="236" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
236
</td>
<td class="new_line diff-line-num" data-linenumber="236" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
236
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC236" class="line" lang="cmake"> <span class="nf" style="color: #990000; font-weight: 600;">PCL_CHECK_FOR_NEON</span><span class="p">()</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="237" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
237
</td>
<td class="new_line diff-line-num" data-linenumber="237" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
237
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC237" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span><span class="p">(</span><span class="si" style="color: #dd1144;">${</span><span class="nv" style="color: #008080;">HAVE_NEON_EXTENSIONS</span><span class="si" style="color: #dd1144;">}</span><span class="p">)</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="238" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
238
</td>
<td class="new_line diff-line-num" data-linenumber="238" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
238
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC238" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_definitions</span> <span class="p">(</span>-D_SLKP_USE_ARM_NEON<span class="p">)</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="239" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
239
</td>
<td class="new_line diff-line-num old" data-linenumber="239" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC239" class="line" lang="cmake"></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="239" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
239
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC239" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>DEFAULT_COMPILE_FLAGS <span class="s2" style="color: #dd1144;">"</span><span class="si" style="color: #dd1144;">${</span><span class="nv" style="color: #008080;">DEFAULT_COMPILE_FLAGS</span><span class="si" style="color: #dd1144;">}</span><span class="s2" style="color: #dd1144;"> -mcpu=native -mtune=native "</span><span class="p">)</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="240" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
240
</td>
<td class="new_line diff-line-num" data-linenumber="240" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
240
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC240" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span><span class="si" style="color: #dd1144;">${</span><span class="nv" style="color: #008080;">HAVE_NEON_EXTENSIONS</span><span class="si" style="color: #dd1144;">}</span><span class="p">)</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="241" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
241
</td>
<td class="new_line diff-line-num" data-linenumber="241" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
241
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC241" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span>NOT NONEON<span class="p">)</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="242" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
242
</td>
<td class="new_line diff-line-num" data-linenumber="242" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
242
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC242" class="line" lang="cmake"></span>
</pre></td>
</tr>
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="284" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="284" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -284,6 +284,8 @@ if (CMAKE_CXX_COMPILER_ID MATCHES "Clang")</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="284" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
284
</td>
<td class="new_line diff-line-num" data-linenumber="284" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
284
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC284" class="line" lang="cmake"> <span class="nf" style="color: #990000; font-weight: 600;">PCL_CHECK_FOR_NEON</span><span class="p">()</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="285" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
285
</td>
<td class="new_line diff-line-num" data-linenumber="285" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
285
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC285" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span><span class="p">(</span><span class="si" style="color: #dd1144;">${</span><span class="nv" style="color: #008080;">HAVE_NEON_EXTENSIONS</span><span class="si" style="color: #dd1144;">}</span><span class="p">)</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="286" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
286
</td>
<td class="new_line diff-line-num" data-linenumber="286" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
286
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC286" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_definitions</span> <span class="p">(</span>-D_SLKP_USE_ARM_NEON<span class="p">)</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="287" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="287" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
287
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC287" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>DEFAULT_COMPILE_FLAGS <span class="s2" style="color: #dd1144;">"</span><span class="si" style="color: #dd1144;">${</span><span class="nv" style="color: #008080;">DEFAULT_COMPILE_FLAGS</span><span class="si" style="color: #dd1144;">}</span><span class="s2" style="color: #dd1144;"> -mcpu=native -mtune=native "</span><span class="p">)</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="287" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="288" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
288
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC288" class="line" lang="cmake"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="287" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
287
</td>
<td class="new_line diff-line-num" data-linenumber="289" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
289
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC289" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span><span class="si" style="color: #dd1144;">${</span><span class="nv" style="color: #008080;">HAVE_NEON_EXTENSIONS</span><span class="si" style="color: #dd1144;">}</span><span class="p">)</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="288" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
288
</td>
<td class="new_line diff-line-num" data-linenumber="290" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
290
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC290" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span>NOT NONEON<span class="p">)</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="289" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
289
</td>
<td class="new_line diff-line-num" data-linenumber="291" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
291
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC291" class="line" lang="cmake"></span>
</pre></td>
</tr>
</table>
<br>
</li>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/65547ade91167ae6589a244327500e8e1a4cf100#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong style="font-weight: 600;">README.md</strong></a>
<hr style="overflow: hidden; border: 1px solid #e1e1e1;">
<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#ffffff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -6,8 +6,8 @@ HyPhy is an open-source software package for the analysis of genetic sequences u</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6
</td>
<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="markdown"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7
</td>
<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Quick Start</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
8
</td>
<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
8
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="markdown"></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
9
</td>
<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Install<span class="idiff left right deletion" style="background-color: #fac5cd;"> </span></span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
10
</td>
<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="markdown"><span class="sb" style="color: #dd1144;">`conda install hyphy`</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
9
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC9" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Install</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10" class="line" lang="markdown"><span class="sb" style="color: #dd1144;">`conda install <span class="idiff left right addition" style="background-color: #c7f0d2;">-c bioconda </span>hyphy`</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
11
</td>
<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
11
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC11" class="line" lang="markdown"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
12
</td>
<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
12
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC12" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Run with Command Line Arguments</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
13
</td>
<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
13
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC13" class="line" lang="markdown"><span class="sb" style="color: #dd1144;">`hyphy <method_name> --alignment <path_to_alignment_file> <additional_method_specific_arguments>`</span> </span>
</pre></td>
</tr>
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="63" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="63" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -63,8 +63,7 @@ If building on a heterogeneous cluster with some nodes that do not support auto-</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
63
</td>
<td class="new_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
63
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC63" class="line" lang="markdown">If you're on a UNIX-compatible system, and you're comfortable with GNU make, then run <span class="sb" style="color: #dd1144;">`make`</span> with one of the following build targets:</span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="64" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
64
</td>
<td class="new_line diff-line-num" data-linenumber="64" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
64
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC64" class="line" lang="markdown"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="65" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
65
</td>
<td class="new_line diff-line-num" data-linenumber="65" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
65
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC65" class="line" lang="markdown"><span class="p">+</span> MP or hyphy - build a HyPhy executable (This used to be "HYPHYMP" but is now just "hyphy") using pthreads to do multiprocessing</span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="66" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
66
</td>
<td class="new_line diff-line-num old" data-linenumber="66" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC66" class="line" lang="markdown"><span class="p">+</span> MPI - build a HyPhy executable (HYPHYMPI) using MPI to do multiprocessing</span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="67" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
67
</td>
<td class="new_line diff-line-num old" data-linenumber="66" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC67" class="line" lang="markdown"><span class="p">+</span> HYPHYMPI - build a HyPhy executable (HYPHYMPI) using openMPI </span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
66
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC66" class="line" lang="markdown"><span class="p">+</span> MPI or HYPHYMPI - build a HyPhy executable (HYPHYMPI) using openMPI to do multiprocessing</span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="68" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
68
</td>
<td class="new_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
67
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC67" class="line" lang="markdown"><span class="p">+</span> LIB - build a HyPhy library (libhyphy_mp) using pthreads to do multiprocessing</span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="69" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
69
</td>
<td class="new_line diff-line-num" data-linenumber="68" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
68
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC68" class="line" lang="markdown"><span class="p">-</span> GTEST - build HyPhy's gtest testing executable (HYPHYGTEST)</span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
70
</td>
<td class="new_line diff-line-num" data-linenumber="69" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
69
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC69" class="line" lang="markdown"></span>
</pre></td>
</tr>
</table>
<br>
</li>
<li id="c772592437fe6a7d4e11445521dd00b76827f448">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/65547ade91167ae6589a244327500e8e1a4cf100#c772592437fe6a7d4e11445521dd00b76827f448"><strong style="font-weight: 600;">res/TemplateBatchFiles/CleanStopCodons.bf</strong></a>
<hr style="overflow: hidden; border: 1px solid #e1e1e1;">
<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#ffffff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="94" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="94" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -94,12 +94,13 @@ for (k=0; k<all64.species; k+= 1) {</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
94
</td>
<td class="new_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
94
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC94" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> sequenceNames </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">k</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = newName;</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
95
</td>
<td class="new_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
95
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC95" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
96
</td>
<td class="new_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
96
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC96" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> else {</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="97" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
97
</td>
<td class="new_line diff-line-num old" data-linenumber="97" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC97" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> sequenceNames </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">k</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = seqName;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="97" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
97
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC97" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"><span class="idiff left right addition" style="background-color: #c7f0d2;"> </span> sequenceNames </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">k</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = seqName;</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
98
</td>
<td class="new_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
98
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC98" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="99" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
99
</td>
<td class="new_line diff-line-num" data-linenumber="99" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
99
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC99" class="line" lang="brainfuck"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="100" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
100
</td>
<td class="new_line diff-line-num" data-linenumber="100" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
100
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC100" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> seqNamesListAll</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">testName</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = 1;</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
101
</td>
<td class="new_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
101
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC101" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="102" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
102
</td>
<td class="new_line diff-line-num" data-linenumber="102" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
102
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC102" class="line" lang="brainfuck"></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
103
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC103" class="line" lang="brainfuck"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="103" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
103
</td>
<td class="new_line diff-line-num" data-linenumber="104" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
104
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC104" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">GetInformation (sequenceData</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> all64);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="104" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
104
</td>
<td class="new_line diff-line-num" data-linenumber="105" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
105
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC105" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">GetDataInfo (duplicateMapper</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> all64);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="105" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
105
</td>
<td class="new_line diff-line-num" data-linenumber="106" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
106
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC106" class="line" lang="brainfuck"></span>
</pre></td>
</tr>
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="118" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="119" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -118,78 +119,99 @@ all64.unique_sites = Rows (all64.site_freqs) * Columns (all64.site_freqs);</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="118" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
118
</td>
<td class="new_line diff-line-num" data-linenumber="119" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
119
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC119" class="line" lang="brainfuck"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="119" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
119
</td>
<td class="new_line diff-line-num" data-linenumber="120" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
120
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC120" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">for (sequenceIndex = 0; sequenceIndex </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> all64</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">species; sequenceIndex </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1) {</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="120" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
120
</td>
<td class="new_line diff-line-num" data-linenumber="121" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
121
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC121" class="line" lang="brainfuck"></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="121" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
121
</td>
<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC121" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">stopCodonCount = 0;</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
122
</td>
<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC122" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">sitesWithDeletions = {1</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">all64</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">unique_sites};</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="123" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
123
</td>
<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC123" class="line" lang="brainfuck"></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="124" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
124
</td>
<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC124" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">for (siteIndex = 0; siteIndex </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> all64</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">unique_sites; siteIndex </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1) {</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
125
</td>
<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC125" class="line" lang="brainfuck"></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
126
</td>
<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC126" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> GetDataInfo (siteInfo</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> all64</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> sequenceIndex</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> siteIndex);</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="127" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
127
</td>
<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC127" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> siteInfo1 = stopCodonTemplate*siteInfo;</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="128" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
128
</td>
<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC128" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> siteInfo2 = nonStopCodonTemplate*siteInfo;</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="129" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
129
</td>
<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC129" class="line" lang="brainfuck"></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="130" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
130
</td>
<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC130" class="line" lang="brainfuck"></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="131" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
131
</td>
<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC131" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (siteInfo1</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">0</span><span class="p">]</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;">0 && siteInfo2</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> == 0) {</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="132" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
132
</td>
<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC132" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> sitesWithDeletions</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">siteIndex</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = 1;</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="133" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
133
</td>
<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC133" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> stopCodonCount </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1;</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="134" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
134
</td>
<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC134" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="135" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
135
</td>
<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC135" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (filteringOption % 2) {</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="136" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
136
</td>
<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC136" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (haveInfoAtSites</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">siteIndex</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> == 0) {</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="137" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
137
</td>
<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC137" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (siteInfo1</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">0</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">siteInfo2</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">stopCodonTemplate) {</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="138" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
138
</td>
<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC138" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> haveInfoAtSites</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">siteIndex</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = 1;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
122
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC122" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> stopCodonCount = 0;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
123
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC123" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> sitesWithDeletions = {1</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">all64</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">unique_sites};</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="124" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
124
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC124" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
125
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC125" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> COUNT_GAPS_IN_FREQUENCIES = 0;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
126
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC126" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
127
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC127" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (siteIndex = 0; siteIndex </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> all64</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">unique_sites; siteIndex </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1) {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
128
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC128" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="129" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
129
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC129" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> GetDataInfo (siteInfo</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> all64</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> sequenceIndex</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> siteIndex);</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
130
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC130" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
131
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC131" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
132
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC132" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> siteInfo1 = stopCodonTemplate*siteInfo;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="133" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
133
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC133" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> siteInfo2 = nonStopCodonTemplate*siteInfo;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="134" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
134
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC134" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="135" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
135
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC135" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="136" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
136
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC136" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (siteInfo1</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">0</span><span class="p">]</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;">0 && siteInfo2</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> == 0) {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
137
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC137" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> sitesWithDeletions</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">siteIndex</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = 1;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
138
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC138" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> stopCodonCount </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
139
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC139" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="140" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
140
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC140" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="141" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
141
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC141" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (filteringOption % 2) {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="142" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
142
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC142" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (haveInfoAtSites</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">siteIndex</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> == 0) {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
143
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC143" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (siteInfo1</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">0</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">siteInfo2</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> 0) {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
144
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC144" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> haveInfoAtSites</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">siteIndex</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = 1;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
145
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC145" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
139
</td>
<td class="new_line diff-line-num" data-linenumber="146" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
146
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC146" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="140" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
140
</td>
<td class="new_line diff-line-num" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
147
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC147" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="141" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
141
</td>
<td class="new_line diff-line-num" data-linenumber="148" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
148
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC148" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="142" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
142
</td>
<td class="new_line diff-line-num old" data-linenumber="149" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC142" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="143" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
143
</td>
<td class="new_line diff-line-num old" data-linenumber="149" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC143" class="line" lang="brainfuck"></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
144
</td>
<td class="new_line diff-line-num old" data-linenumber="149" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC144" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">if (stopCodonCount </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> 0) {</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="145" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
145
</td>
<td class="new_line diff-line-num old" data-linenumber="149" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC145" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (filterinOption == 4) {</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="146" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
146
</td>
<td class="new_line diff-line-num old" data-linenumber="149" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC146" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> continue;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
149
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC149" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
150
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC150" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (stopCodonCount </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> 0) {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
151
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC151" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (filterinOption == 4) {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
152
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC152" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> continue;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
153
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC153" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
154
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC154" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> fprintf (stdout</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "\nSequence "</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> sequenceNames</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceIndex</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> ":");</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
155
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC155" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> fprintf (stdout</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "\n\t"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> Format(stopCodonCount</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">8</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">0)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> " stop codons found</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">");</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
156
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC156" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="157" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
157
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC157" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> doSomething = 1;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="158" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
158
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC158" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> cleanedString = "";</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
159
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC159" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> seqString = sequenceData</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceIndex</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
160
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC160" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> cleanedString * (Abs(seqString)</span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">1);</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="161" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
161
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC161" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
162
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC162" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (siteIndex = 0; siteIndex </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> all64</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">sites; siteIndex </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1) {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="163" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
163
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC163" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> stopCodonCount = duplicateMapper</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">siteIndex</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="164" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
164
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC164" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (sitesWithDeletions</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">stopCodonCount</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">) {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
165
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC165" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> cleanedString * replacementString;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
166
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC166" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="167" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
167
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC167" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> cleanedString * seqString</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">3*siteIndex</span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;">3*siteIndex</span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
168
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC168" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
169
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC169" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
170
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC170" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> cleanedString * 0;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="171" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
171
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC171" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> sequenceData</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceIndex</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = cleanedString;</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
147
</td>
<td class="new_line diff-line-num" data-linenumber="172" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
172
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC172" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="148" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
148
</td>
<td class="new_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC148" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> fprintf (stdout</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "\nSequence "</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> sequenceNames</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceIndex</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> ":");</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="149" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
149
</td>
<td class="new_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC149" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> fprintf (stdout</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "\n\t"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> Format(stopCodonCount</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">8</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">0)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> " stop codons found</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">");</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
150
</td>
<td class="new_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC150" class="line" lang="brainfuck"></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="151" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
151
</td>
<td class="new_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC151" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> doSomething = 1;</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="152" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
152
</td>
<td class="new_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC152" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> cleanedString = "";</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="153" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
153
</td>
<td class="new_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC153" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> seqString = sequenceData</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceIndex</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="154" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
154
</td>
<td class="new_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC154" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> cleanedString * (Abs(seqString)</span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">1);</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="155" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
155
</td>
<td class="new_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC155" class="line" lang="brainfuck"></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="156" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
156
</td>
<td class="new_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC156" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (siteIndex = 0; siteIndex </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> all64</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">sites; siteIndex </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1) {</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="157" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
157
</td>
<td class="new_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC157" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> stopCodonCount = duplicateMapper</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">siteIndex</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="158" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
158
</td>
<td class="new_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC158" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (sitesWithDeletions</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">stopCodonCount</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">) {</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="159" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
159
</td>
<td class="new_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC159" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> cleanedString * replacementString;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="173" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
173
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC173" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
174
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC174" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="175" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
175
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC175" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
176
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC176" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (filteringOption </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;">= 2) {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="177" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
177
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC177" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (duplicateChecker</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceData</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceIndex</span><span class="p">]]</span><span class="c1" style="color: #999988; font-style: italic;"> == 0) {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
178
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC178" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> duplicateChecker</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceData</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceIndex</span><span class="p">]]</span><span class="c1" style="color: #999988; font-style: italic;"> = 1;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="179" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
179
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC179" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> notDuplicate</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceIndex</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = 1;</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="160" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
160
</td>
<td class="new_line diff-line-num" data-linenumber="180" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
180
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC180" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="161" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
161
</td>
<td class="new_line diff-line-num old" data-linenumber="181" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC161" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff left deletion" style="background-color: #fac5cd;">cleanedString * seqString</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">[</span></span><span class="c1" style="color: #999988; font-style: italic;"><span class="idiff deletion" style="background-color: #fac5cd;">3*siteIndex</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">][</span></span><span class="c1" style="color: #999988; font-style: italic;"><span class="idiff deletion" style="background-color: #fac5cd;">3*siteIndex</span></span><span class="nf" style="color: #990000; font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">+</span></span><span class="c1" style="color: #999988; font-style: italic;"><span class="idiff deletion" style="background-color: #fac5cd;">2</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">]</span></span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
181
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC181" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff left right addition" style="background-color: #c7f0d2;">doSomething = 1</span>;</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="162" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
162
</td>
<td class="new_line diff-line-num" data-linenumber="182" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
182
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC182" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
163
</td>
<td class="new_line diff-line-num old" data-linenumber="183" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC163" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="164" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
164
</td>
<td class="new_line diff-line-num old" data-linenumber="183" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC164" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> cleanedString * 0;</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="165" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
165
</td>
<td class="new_line diff-line-num old" data-linenumber="183" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC165" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> sequenceData</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceIndex</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = cleanedString;</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="166" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
166
</td>
<td class="new_line diff-line-num old" data-linenumber="183" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC166" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="167" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
167
</td>
<td class="new_line diff-line-num old" data-linenumber="183" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC167" class="line" lang="brainfuck"></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="168" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
168
</td>
<td class="new_line diff-line-num old" data-linenumber="183" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC168" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">if (filteringOption </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;">= 2) {</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="169" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
169
</td>
<td class="new_line diff-line-num old" data-linenumber="183" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC169" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (duplicateChecker</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceData</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceIndex</span><span class="p">]]</span><span class="c1" style="color: #999988; font-style: italic;"> == 0) {</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
170
</td>
<td class="new_line diff-line-num old" data-linenumber="183" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC170" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> duplicateChecker</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceData</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceIndex</span><span class="p">]]</span><span class="c1" style="color: #999988; font-style: italic;"> = 1;</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="171" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
171
</td>
<td class="new_line diff-line-num old" data-linenumber="183" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC171" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> notDuplicate</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceIndex</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = 1;</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="172" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
172
</td>
<td class="new_line diff-line-num" data-linenumber="183" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
183
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC183" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
173
</td>
<td class="new_line diff-line-num old" data-linenumber="184" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC173" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff left right deletion" style="background-color: #fac5cd;">doSomething = 1;</span></span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="184" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
184
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC184" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff left addition" style="background-color: #c7f0d2;">notDuplicate</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">[</span></span><span class="c1" style="color: #999988; font-style: italic;"><span class="idiff addition" style="background-color: #c7f0d2;">sequenceIndex</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">]</span></span><span class="c1" style="color: #999988; font-style: italic;"><span class="idiff right addition" style="background-color: #c7f0d2;"> = 1; </span></span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="174" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
174
</td>
<td class="new_line diff-line-num" data-linenumber="185" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
185
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC185" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="175" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
175
</td>
<td class="new_line diff-line-num old" data-linenumber="186" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC175" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">} else {</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="176" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
176
</td>
<td class="new_line diff-line-num old" data-linenumber="186" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC176" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> notDuplicate</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceIndex</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = 1; }</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="177" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
177
</td>
<td class="new_line diff-line-num" data-linenumber="186" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
186
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC186" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="178" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
178
</td>
<td class="new_line diff-line-num" data-linenumber="187" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
187
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC187" class="line" lang="brainfuck"></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="179" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
188
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC188" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">filterSites = 0;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="179" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="189" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
189
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC189" class="line" lang="brainfuck"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="179" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
179
</td>
<td class="new_line diff-line-num" data-linenumber="190" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
190
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC190" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">if (filteringOption%2) {</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="180" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
180
</td>
<td class="new_line diff-line-num old" data-linenumber="191" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC180" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> doSomething = doSomething || (Abs(haveInfoAtSites)</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;">all64</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">unique_sites);</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="191" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
191
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC191" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> filterSites = Abs(haveInfoAtSites)</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;">all64</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">unique_sites;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="192" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
192
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC192" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> doSomething = doSomething || filterSites;</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="181" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
181
</td>
<td class="new_line diff-line-num" data-linenumber="193" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
193
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC193" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="182" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
182
</td>
<td class="new_line diff-line-num" data-linenumber="194" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
194
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC194" class="line" lang="brainfuck"></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="183" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
183
</td>
<td class="new_line diff-line-num old" data-linenumber="195" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC183" class="line" lang="brainfuck"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="184" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
184
</td>
<td class="new_line diff-line-num" data-linenumber="195" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
195
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC195" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">if (!doSomething) {</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="185" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
185
</td>
<td class="new_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
196
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC196" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> fprintf (stdout</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "\n\nNo stop codons found\n\n");</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="186" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
186
</td>
<td class="new_line diff-line-num" data-linenumber="197" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
197
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC197" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="187" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
187
</td>
<td class="new_line diff-line-num" data-linenumber="198" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
198
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC198" class="line" lang="brainfuck"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="188" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
188
</td>
<td class="new_line diff-line-num" data-linenumber="199" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
199
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC199" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">SetDialogPrompt ("Save cleaned data to:");</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="189" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
189
</td>
<td class="new_line diff-line-num" data-linenumber="200" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
200
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC200" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">fprintf (PROMPT_FOR_FILE</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> CLEAR_FILE</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> KEEP_OPEN);</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="190" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="201" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
201
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC201" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">seqLen = Abs (sequenceData</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="190" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
190
</td>
<td class="new_line diff-line-num" data-linenumber="202" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
202
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC202" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">for (sequenceIndex = 0; sequenceIndex </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> all64</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">species; sequenceIndex </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1) {</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="191" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
191
</td>
<td class="new_line diff-line-num" data-linenumber="203" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
203
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC203" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (notDuplicate</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceIndex</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">) {</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="192" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
192
</td>
<td class="new_line diff-line-num old" data-linenumber="204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC192" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> fprintf (LAST_FILE_PATH</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;">"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> sequenceNames</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceIndex</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "\n"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> sequenceData</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceIndex</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "\n\n");</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
204
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC204" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (filterSites) {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="205" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
205
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC205" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> fprintf (LAST_FILE_PATH</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;">"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> sequenceNames</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceIndex</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "\n");</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="206" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
206
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC206" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (s = 0; s </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> seqLen; s</span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">=3) {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="207" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
207
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC207" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (haveInfoAtSites</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">duplicateMapper</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">s$3</span><span class="p">]]</span><span class="c1" style="color: #999988; font-style: italic;">) {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="208" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
208
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC208" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> fprintf (LAST_FILE_PATH</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> (sequenceData</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceIndex</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">s</span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;">s</span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">);</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="209" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
209
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC209" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
210
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC210" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="211" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
211
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC211" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> fprintf (LAST_FILE_PATH</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "\n\n");</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="212" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
212
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC212" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="213" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
213
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC213" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> fprintf (LAST_FILE_PATH</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;">"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> sequenceNames</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceIndex</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "\n"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> sequenceData</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">sequenceIndex</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "\n\n");</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="214" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
214
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC214" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="193" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
193
</td>
<td class="new_line diff-line-num" data-linenumber="215" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
215
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC215" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="194" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
194
</td>
<td class="new_line diff-line-num" data-linenumber="216" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
216
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC216" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="195" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
195
</td>
<td class="new_line diff-line-num" data-linenumber="217" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
217
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC217" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">fprintf (LAST_FILE_PATH</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> CLOSE_FILE);</span></span>
</pre></td>
</tr>
</table>
<br>
</li>
<li id="bc98d7300147ce39ef8ee0f9b35f3252bebd01d2">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/65547ade91167ae6589a244327500e8e1a4cf100#bc98d7300147ce39ef8ee0f9b35f3252bebd01d2"><strong style="font-weight: 600;">res/TemplateBatchFiles/SelectionAnalyses/MEME.bf</strong></a>
<hr style="overflow: hidden; border: 1px solid #e1e1e1;">
<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#ffffff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="752" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="752" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -752,7 +752,6 @@ for (meme.partition_index = 0; meme.partition_index < meme.partition_count; meme</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="752" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
752
</td>
<td class="new_line diff-line-num" data-linenumber="752" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
752
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC752" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="753" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
753
</td>
<td class="new_line diff-line-num" data-linenumber="753" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
753
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC753" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "meme</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">store_results");</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="754" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
754
</td>
<td class="new_line diff-line-num" data-linenumber="754" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
754
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC754" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
755
</td>
<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC755" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> pattern_count_all</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="756" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
756
</td>
<td class="new_line diff-line-num" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
755
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC755" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> '</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="757" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
757
</td>
<td class="new_line diff-line-num" data-linenumber="756" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
756
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC756" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> );</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="758" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
758
</td>
<td class="new_line diff-line-num" data-linenumber="757" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
757
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC757" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1724" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1723" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1724,7 +1723,7 @@ lfunction meme.store_results (node, result, arguments) {</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1724" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1724
</td>
<td class="new_line diff-line-num" data-linenumber="1723" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1723
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1723" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (has_psi) {</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1725" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1725
</td>
<td class="new_line diff-line-num" data-linenumber="1724" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1724
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1724" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> result_row</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">has_psi</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = estimators</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">GetGlobalMLE (result</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">utility</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alternative")</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">^"terms</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">meme</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fg_param_prefix"</span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> ^"terms</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">parameters</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">triple_hit_rate");</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1726" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1726
</td>
<td class="new_line diff-line-num" data-linenumber="1725" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1725
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1725" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (None == result_row</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">has_psi</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">) {</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1727" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1727
</td>
<td class="new_line diff-line-num old" data-linenumber="1726" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1727" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> result_row</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">has_<span class="idiff left right deletion" style="background-color: #fac5cd;">delta</span></span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = ((scalers</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">'BG'</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">^"terms</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">parameters</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">triple_hit_rate"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"scaler"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1728" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1726" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1726
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1726" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> result_row</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">has_<span class="idiff left right addition" style="background-color: #c7f0d2;">psi</span></span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = ((scalers</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">'BG'</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">^"terms</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">parameters</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">triple_hit_rate"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"scaler"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1728" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1728
</td>
<td class="new_line diff-line-num" data-linenumber="1727" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1727
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1727" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1729" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1729
</td>
<td class="new_line diff-line-num" data-linenumber="1728" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1728
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1728" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> ^"meme</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">site_multihit_string" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= "/" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> Format (result_row</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">has_psi</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">0</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1730" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1730
</td>
<td class="new_line diff-line-num" data-linenumber="1729" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1729
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1729" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
</table>
<br>
</li>
<li id="80cb7c212661a2afbd05c16dce9f84f45709578e">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/65547ade91167ae6589a244327500e8e1a4cf100#80cb7c212661a2afbd05c16dce9f84f45709578e"><strong style="font-weight: 600;">res/TemplateBatchFiles/SelectionAnalyses/PRIME.bf</strong></a>
<hr style="overflow: hidden; border: 1px solid #e1e1e1;">
<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#ffffff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="545" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="545" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -545,7 +545,10 @@ for (prime.partition_index = 0; prime.partition_index < prime.partition_count; p</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="545" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
545
</td>
<td class="new_line diff-line-num" data-linenumber="545" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
545
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC545" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> /* run the main loop over all unique site pattern combinations */</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="546" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
546
</td>
<td class="new_line diff-line-num" data-linenumber="546" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
546
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC546" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="547" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
547
</td>
<td class="new_line diff-line-num" data-linenumber="547" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
547
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC547" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">pattern_count = 1;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="548" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="548" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
548
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC548" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="548" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="549" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
549
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC549" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="548" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
548
</td>
<td class="new_line diff-line-num" data-linenumber="550" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
550
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC550" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (_pattern_</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> _pattern_info_; in; prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">site_patterns) {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="549" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="551" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
551
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC551" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="549" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
549
</td>
<td class="new_line diff-line-num" data-linenumber="552" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
552
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC552" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> io</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ReportProgressBar(""</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "Working on site pattern " </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> (prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">pattern_count) </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> "/" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> Abs (prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">site_patterns));</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="550" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
550
</td>
<td class="new_line diff-line-num" data-linenumber="553" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
553
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC553" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (_pattern_info_</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">utility</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">data</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">is_constant")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">) {</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="551" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
551
</td>
<td class="new_line diff-line-num" data-linenumber="554" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
554
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC554" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">store_results (</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">1</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">None</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">{"0" : "prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">site_likelihood"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
</pre></td>
</tr>
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="556" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="559" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -556,6 +559,7 @@ for (prime.partition_index = 0; prime.partition_index < prime.partition_count; p</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="556" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
556
</td>
<td class="new_line diff-line-num" data-linenumber="559" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
559
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC559" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "5" : prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">site_model_mapping</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="557" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
557
</td>
<td class="new_line diff-line-num" data-linenumber="560" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
560
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC560" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> });</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="558" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
558
</td>
<td class="new_line diff-line-num" data-linenumber="561" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
561
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC561" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="559" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="562" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
562
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC562" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="559" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
559
</td>
<td class="new_line diff-line-num" data-linenumber="563" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
563
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC563" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> mpi</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">QueueJob (prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">queue</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">handle_a_site"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> {"0" : "prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">site_likelihood"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="560" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
560
</td>
<td class="new_line diff-line-num" data-linenumber="564" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
564
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC564" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "1" : "prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">site_likelihood_property"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="561" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
561
</td>
<td class="new_line diff-line-num" data-linenumber="565" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
565
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC565" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "2" : alignments</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">serialize_site_filter</span></span>
</pre></td>
</tr>
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="703" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="707" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -703,6 +707,8 @@ lfunction prime.handle_a_site (lf_fel, lf_prop, filter_data, partition_index, pa</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="703" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
703
</td>
<td class="new_line diff-line-num" data-linenumber="707" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
707
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC707" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> //Export (lfe</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> ^lf_prop);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="704" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
704
</td>
<td class="new_line diff-line-num" data-linenumber="708" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
708
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC708" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> // fprintf ("/tmp/PRIME</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">site</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> (pattern_info</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"sites"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> "</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">bf"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">CLEAR_FILE</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">lfe);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="705" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
705
</td>
<td class="new_line diff-line-num" data-linenumber="709" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
709
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC709" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="706" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="710" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
710
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC710" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> character_map = None; </span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="706" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="711" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
711
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC711" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="706" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
706
</td>
<td class="new_line diff-line-num" data-linenumber="712" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
712
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC712" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (^"prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">site_beta" </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> 0) {</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="707" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
707
</td>
<td class="new_line diff-line-num" data-linenumber="713" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
713
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC713" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="708" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
708
</td>
<td class="new_line diff-line-num" data-linenumber="714" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
714
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC714" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> // fit the universal alternative</span></span>
</pre></td>
</tr>
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="781" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="787" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -781,8 +787,8 @@ lfunction prime.handle_a_site (lf_fel, lf_prop, filter_data, partition_index, pa</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="781" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
781
</td>
<td class="new_line diff-line-num" data-linenumber="787" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
787
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC787" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "OPTIMIZATION_PRECISION": 1e</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">3</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="782" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
782
</td>
<td class="new_line diff-line-num" data-linenumber="788" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
788
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC788" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> });</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="783" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
783
</td>
<td class="new_line diff-line-num" data-linenumber="789" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
789
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC789" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="784" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
784
</td>
<td class="new_line diff-line-num old" data-linenumber="790" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC784" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> //<span class="idiff left right deletion" style="background-color: #fac5cd;"> </span>Export (lfe</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> ^lf_prop);</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="785" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
785
</td>
<td class="new_line diff-line-num old" data-linenumber="790" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC785" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> //<span class="idiff left right deletion" style="background-color: #fac5cd;"> </span>fprintf ("/tmp/PRIME</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">site</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> (pattern_info</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"sites"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> "</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">bf"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">CLEAR_FILE</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">lfe);</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="790" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
790
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC790" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> //Export (lfe</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> ^lf_prop);</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="791" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
791
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC791" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> //fprintf ("/tmp/PRIME</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">site</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> (pattern_info</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"sites"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> "</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">bf"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">CLEAR_FILE</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">lfe);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="786" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
786
</td>
<td class="new_line diff-line-num" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
792
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC792" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="787" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
787
</td>
<td class="new_line diff-line-num" data-linenumber="793" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
793
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC793" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> //console</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">log ("\n" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> ^"LF_INITIAL_GRID_MAXIMUM_VALUE" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> "\nGrid best"</span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> ^"LF_INITIAL_GRID_MAXIMUM" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> " / optimized " </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> results</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">1</span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> "\n");</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="788" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
788
</td>
<td class="new_line diff-line-num" data-linenumber="794" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
794
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC794" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> Optimize (results</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> ^lf_prop);</span></span>
</pre></td>
</tr>
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="878" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="884" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -878,25 +884,41 @@ lfunction prime.handle_a_site (lf_fel, lf_prop, filter_data, partition_index, pa</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="878" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
878
</td>
<td class="new_line diff-line-num" data-linenumber="884" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
884
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC884" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> //console</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">log ("\nPRIME = " </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> altL);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="879" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
879
</td>
<td class="new_line diff-line-num" data-linenumber="885" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
885
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC885" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> //console</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">log ("alpha = " </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> ^"prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">site_alpha");</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="880" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
880
</td>
<td class="new_line diff-line-num" data-linenumber="886" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
886
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC886" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> //console</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">log ("beta = " </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> ^"prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">site_beta");</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="881" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
881
</td>
<td class="new_line diff-line-num old" data-linenumber="887" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC881" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="882" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
882
</td>
<td class="new_line diff-line-num old" data-linenumber="887" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC882" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff left right deletion" style="background-color: #fac5cd;">character_map = None; </span></span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="883" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="887" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
887
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC887" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span></span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="883" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="888" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
888
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC888" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="883" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
883
</td>
<td class="new_line diff-line-num" data-linenumber="889" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
889
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC889" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (^"prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">impute_states") {</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="884" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
884
</td>
<td class="new_line diff-line-num" data-linenumber="890" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
890
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC890" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> DataSet anc = ReconstructAncestors ( ^lf_prop</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> {{0}}</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> MARGINAL</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> DOLEAVES);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="885" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
885
</td>
<td class="new_line diff-line-num" data-linenumber="891" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
891
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC891" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> GetString (names</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> anc</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">1);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="886" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
886
</td>
<td class="new_line diff-line-num" data-linenumber="892" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
892
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC892" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> GetDataInfo (codon_chars</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> ^((lfInfo</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"Datafilters"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">) </span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "CHARACTERS");</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="887" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="893" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
893
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC893" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> GetString (names_obs</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> ^((lfInfo</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"Datafilters"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">1);</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="887" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="894" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
894
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC894" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> names_obs = utility</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MatrixToDict (names_obs);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="887" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
887
</td>
<td class="new_line diff-line-num" data-linenumber="895" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
895
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC895" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="888" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="896" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
896
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC896" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="888" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
888
</td>
<td class="new_line diff-line-num" data-linenumber="897" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
897
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC897" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> character_map = {};</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="889" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
889
</td>
<td class="new_line diff-line-num" data-linenumber="898" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
898
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC898" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (seq_id</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> seq_name; in; names) {</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="890" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
890
</td>
<td class="new_line diff-line-num old" data-linenumber="899" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC890" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> character_map </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">seq_name</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = {};</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="891" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="899" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
899
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC899" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> GetDataInfo (site_map</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> ^((lfInfo</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"Datafilters"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> names_obs</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">seq_name</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 0);</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="891" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="900" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
900
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC900" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> character_map </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">seq_name</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = {'observed' :{} </span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 'imputed' : {}</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 'support' : 0};</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="891" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="901" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
901
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC901" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="891" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="902" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
902
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC902" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="891" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="903" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
903
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC903" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (char</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> char_support; in; site_map) {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="891" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="904" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
904
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC904" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (char_support </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> 1e</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">6) {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="891" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="905" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
905
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC905" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> (((character_map </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">seq_name</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">))</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">'observed'</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">codon_chars</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">char</span><span class="p">]]</span><span class="c1" style="color: #999988; font-style: italic;"> = char_support;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="891" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="906" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
906
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC906" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="891" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="907" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
907
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC907" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="891" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="908" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
908
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC908" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="891" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
891
</td>
<td class="new_line diff-line-num" data-linenumber="909" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
909
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC909" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (char</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> char_support; in; (anc</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">marginal_support_matrix)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">seq_id</span><span class="p">][</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">) {</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="892" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
892
</td>
<td class="new_line diff-line-num" data-linenumber="910" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
910
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC910" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (char_support </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> 1e</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">6) {</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="893" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
893
</td>
<td class="new_line diff-line-num old" data-linenumber="911" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC893" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> (character_map </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">seq_name</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">codon_chars</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">char</span><span class="p">]]</span><span class="c1" style="color: #999988; font-style: italic;"> = char_support;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="894" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="911" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
911
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC911" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> (((character_map </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">seq_name</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">))</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">'imputed'</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">codon_chars</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">char</span><span class="p">]]</span><span class="c1" style="color: #999988; font-style: italic;"> = char_support;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="894" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="912" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
912
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC912" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if ( (((character_map </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">seq_name</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">))</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">'observed'</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">codon_chars</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">char</span><span class="p">]]</span><span class="c1" style="color: #999988; font-style: italic;">) {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="894" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="913" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
913
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC913" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> (character_map </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">seq_name</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">'support'</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= char_support;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="894" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="914" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
914
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC914" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="894" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
894
</td>
<td class="new_line diff-line-num" data-linenumber="915" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
915
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC915" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="895" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
895
</td>
<td class="new_line diff-line-num" data-linenumber="916" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
916
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC916" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="896" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="917" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
917
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC917" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="896" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
896
</td>
<td class="new_line diff-line-num" data-linenumber="918" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
918
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC918" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="897" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
897
</td>
<td class="new_line diff-line-num old" data-linenumber="919" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC897" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="898" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
898
</td>
<td class="new_line diff-line-num" data-linenumber="919" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
919
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC919" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="899" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
899
</td>
<td class="new_line diff-line-num" data-linenumber="920" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
920
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC920" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="900" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="921" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
921
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC921" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="900" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
900
</td>
<td class="new_line diff-line-num" data-linenumber="922" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
922
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC922" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> utility</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ToggleEnvVariable ("TOLERATE_CONSTRAINT_VIOLATION"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> None); </span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="901" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
901
</td>
<td class="new_line diff-line-num" data-linenumber="923" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
923
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC923" class="line" lang="brainfuck"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="902" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
902
</td>
<td class="new_line diff-line-num" data-linenumber="924" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
924
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC924" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> ancestral_info = ancestral</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">build (lf_prop</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">0</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">FALSE);</span></span>
</pre></td>
</tr>
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1138" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1160" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1138,7 +1160,9 @@ lfunction prime.store_results (node, result, arguments) {</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1138" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1138
</td>
<td class="new_line diff-line-num" data-linenumber="1160" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1160
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1160" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> //console</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">log (result_row);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1139
</td>
<td class="new_line diff-line-num" data-linenumber="1161" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1161
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1161" class="line" lang="brainfuck"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1140" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1140
</td>
<td class="new_line diff-line-num" data-linenumber="1162" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1162
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1162" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> utility</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">EnsureKey (^"prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">site_results"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> partition_index);</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1141" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1141
</td>
<td class="new_line diff-line-num old" data-linenumber="1163" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1141" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> utility</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">EnsureKey (^"prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">imputed_leaf_states"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> partition_index);</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1142" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1163" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1163
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1163" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (^"prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">impute_states") {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1142" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1164" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1164
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1164" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> utility</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">EnsureKey (^"prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">imputed_leaf_states"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> partition_index);</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1142" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1165" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1165
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1165" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1142" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1142
</td>
<td class="new_line diff-line-num" data-linenumber="1166" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1166
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1166" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> utility</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">EnsureKey (^"prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">sub_mapping"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> partition_index);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1143" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1143
</td>
<td class="new_line diff-line-num" data-linenumber="1167" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1167
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1167" class="line" lang="brainfuck"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1144" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1144
</td>
<td class="new_line diff-line-num" data-linenumber="1168" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1168
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1168" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> sites_mapping_to_pattern = pattern_info</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">utility</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">data</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">sites")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
</pre></td>
</tr>
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1148" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1172" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1148,7 +1172,9 @@ lfunction prime.store_results (node, result, arguments) {</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1148" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1148
</td>
<td class="new_line diff-line-num" data-linenumber="1172" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1172
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1172" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> site_index = sites_mapping_to_pattern</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">i</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1149" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1149
</td>
<td class="new_line diff-line-num" data-linenumber="1173" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1173
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1173" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> ((^"prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">site_results")</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">site_index</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = result_row;</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1150" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1150
</td>
<td class="new_line diff-line-num" data-linenumber="1174" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1174
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1174" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> ((^"prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">sub_mapping")</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">site_index</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = sub_map;</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1151" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1151
</td>
<td class="new_line diff-line-num old" data-linenumber="1175" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1151" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> ((^"prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">imputed_leaf_states")</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">site_index</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = result</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">^"terms</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">prime_imputed_states"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1152" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1175" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1175
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1175" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (^"prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">impute_states") {</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1152" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1176" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1176
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1176" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> ((^"prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">imputed_leaf_states")</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">site_index</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = result</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">^"terms</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">prime_imputed_states"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1152" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1177" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1177
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1177" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1152" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1152
</td>
<td class="new_line diff-line-num" data-linenumber="1178" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1178
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1178" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> prime</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">report</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">echo (site_index</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> partition_index</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> result_row);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1153" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1153
</td>
<td class="new_line diff-line-num" data-linenumber="1179" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1179
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1179" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1154" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1154
</td>
<td class="new_line diff-line-num" data-linenumber="1180" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1180
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1180" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span></pre></td>
</tr>
</table>
<br>
</li>
<li id="02cbcb76e8ce1aa3e72d55e6696cda20813d57b6">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/65547ade91167ae6589a244327500e8e1a4cf100#02cbcb76e8ce1aa3e72d55e6696cda20813d57b6"><strong style="font-weight: 600;">src/core/batchlan.cpp</strong></a>
<hr style="overflow: hidden; border: 1px solid #e1e1e1;">
<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#ffffff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="507" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="507" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -507,11 +507,18 @@ hyBLFunctionType GetBFFunctionType (long idx) {</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="507" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
507
</td>
<td class="new_line diff-line-num" data-linenumber="507" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
507
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC507" class="line" lang="cpp"><span class="p">}</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="508" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
508
</td>
<td class="new_line diff-line-num" data-linenumber="508" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
508
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC508" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="509" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
509
</td>
<td class="new_line diff-line-num" data-linenumber="509" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
509
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC509" class="line" lang="cpp"><span class="c1" style="color: #999988; font-style: italic;">//____________________________________________________________________________________</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="510" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
510
</td>
<td class="new_line diff-line-num old" data-linenumber="510" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC510" class="line" lang="cpp"><span class="n" style="color: #333333;">_String</span> <span class="k" style="font-weight: 600;">const</span> <span class="nf" style="color: #990000; font-weight: 600;">ExportBFFunction</span> <span class="p">(</span><span class="kt" style="color: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">bool</span> <span class="n" style="color: #333333;">recursive</span><span class="p">)</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="511" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="510" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
510
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC510" class="line" lang="cpp"><span class="n" style="color: #333333;">_String</span> <span class="k" style="font-weight: 600;">const</span> <span class="nf" style="color: #990000; font-weight: 600;">ExportBFFunction</span> <span class="p">(</span><span class="kt" style="color: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">bool</span> <span class="n" style="color: #333333;">recursive</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">_AVLList</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">*</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">tracker</span></span><span class="p">)</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="511" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
511
</td>
<td class="new_line diff-line-num" data-linenumber="511" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
511
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC511" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="512" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
512
</td>
<td class="new_line diff-line-num" data-linenumber="512" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
512
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC512" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="513" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
513
</td>
<td class="new_line diff-line-num" data-linenumber="513" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
513
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC513" class="line" lang="cpp"> <span class="n" style="color: #333333;">_StringBuffer</span> <span class="n" style="color: #333333;">bf</span> <span class="p">(</span><span class="mi" style="color: #009999;">8192UL</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="514" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
514
</td>
<td class="new_line diff-line-num" data-linenumber="514" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
514
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC514" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">IsBFFunctionIndexValid</span><span class="p">(</span><span class="n" style="color: #333333;">idx</span><span class="p">))</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="515" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="515" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
515
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC515" class="line" lang="cpp"> </span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="515" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="516" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
516
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC516" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">tracker</span><span class="p">)</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="515" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="517" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
517
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC517" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">tracker</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">FindLong</span> <span class="p">(</span><span class="n" style="color: #333333;">idx</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #009999;">0</span><span class="p">)</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="515" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="518" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
518
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC518" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">bf</span><span class="p">;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="515" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="519" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
519
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC519" class="line" lang="cpp"> <span class="p">}</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="515" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="520" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
520
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC520" class="line" lang="cpp"> <span class="n" style="color: #333333;">tracker</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">InsertNumber</span><span class="p">(</span><span class="n" style="color: #333333;">idx</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="515" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="521" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
521
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC521" class="line" lang="cpp"> <span class="p">}</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="515" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
515
</td>
<td class="new_line diff-line-num" data-linenumber="522" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
522
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC522" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="516" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
516
</td>
<td class="new_line diff-line-num" data-linenumber="523" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
523
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC523" class="line" lang="cpp"> <span class="n" style="color: #333333;">_String</span> <span class="n" style="color: #333333;">hbf_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">GetBFFunctionNameByIndex</span> <span class="p">(</span><span class="n" style="color: #333333;">idx</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="517" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
517
</td>
<td class="new_line diff-line-num" data-linenumber="524" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
524
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC524" class="line" lang="cpp"> <span class="n" style="color: #333333;">_ExecutionList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">body</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333333;">GetBFFunctionBody</span><span class="p">(</span><span class="n" style="color: #333333;">idx</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="567" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="574" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -567,7 +574,7 @@ _String const ExportBFFunction (long idx, bool recursive) {</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="567" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
567
</td>
<td class="new_line diff-line-num" data-linenumber="574" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
574
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC574" class="line" lang="cpp"> <span class="n" style="color: #333333;">bf</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #dd1144;">"</span><span class="se" style="color: #dd1144;">\n</span><span class="s" style="color: #dd1144;">/*----- Called function '"</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="568" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
568
</td>
<td class="new_line diff-line-num" data-linenumber="575" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
575
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC575" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">a_name</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="569" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
569
</td>
<td class="new_line diff-line-num" data-linenumber="576" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
576
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC576" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #dd1144;">"' ------*/</span><span class="se" style="color: #dd1144;">\n</span><span class="s" style="color: #dd1144;">"</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="570" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
570
</td>
<td class="new_line diff-line-num old" data-linenumber="577" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC570" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333333;">ExportBFFunction</span> <span class="p">(</span><span class="n" style="color: #333333;">FindBFFunctionName</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">a_name</span><span class="p">),</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right deletion" style="background-color: #fac5cd;">false</span></span><span class="p">)</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="571" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="577" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
577
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC577" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333333;">ExportBFFunction</span> <span class="p">(</span><span class="n" style="color: #333333;">FindBFFunctionName</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">a_name</span><span class="p">),</span> <span class="n" style="color: #333333;"><span class="idiff left addition" style="background-color: #c7f0d2;">tracker</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">?</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">recursive</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">:</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff addition" style="background-color: #c7f0d2;">false</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">tracker</span></span><span class="p">)</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="571" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
571
</td>
<td class="new_line diff-line-num" data-linenumber="578" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
578
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC578" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #dd1144;">"</span><span class="se" style="color: #dd1144;">\n\n</span><span class="s" style="color: #dd1144;">"</span><span class="p">;</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="572" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
572
</td>
<td class="new_line diff-line-num" data-linenumber="579" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
579
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC579" class="line" lang="cpp"> <span class="p">}</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="573" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
573
</td>
<td class="new_line diff-line-num" data-linenumber="580" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
580
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC580" class="line" lang="cpp"> <span class="p">}</span></span>
</pre></td>
</tr>
</table>
<br>
</li>
<li id="cbedcf5fec686e5f563504b995c5d7d07fd8c6b2">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/65547ade91167ae6589a244327500e8e1a4cf100#cbedcf5fec686e5f563504b995c5d7d07fd8c6b2"><strong style="font-weight: 600;">src/core/batchlanruntime.cpp</strong></a>
<hr style="overflow: hidden; border: 1px solid #e1e1e1;">
<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#ffffff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="887" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="887" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -887,7 +887,8 @@ bool _ElementaryCommand::HandleConstructCategoryMatrix (_ExecutionList& cur</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="887" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
887
</td>
<td class="new_line diff-line-num" data-linenumber="887" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
887
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC887" class="line" lang="cpp"> <span class="n" style="color: #333333;">_String</span> <span class="p">(</span><span class="s" style="color: #dd1144;">"WEIGHTS"</span><span class="p">),</span><span class="n" style="color: #333333;">_hyphyLFConstructCategoryMatrixWeights</span><span class="p">,</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="888" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
888
</td>
<td class="new_line diff-line-num" data-linenumber="888" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
888
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC888" class="line" lang="cpp"> <span class="n" style="color: #333333;">_String</span> <span class="p">(</span><span class="s" style="color: #dd1144;">"SITE_LOG_LIKELIHOODS"</span><span class="p">),</span> <span class="n" style="color: #333333;">_hyphyLFConstructCategoryMatrixSiteProbabilities</span><span class="p">,</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="889" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
889
</td>
<td class="new_line diff-line-num" data-linenumber="889" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
889
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC889" class="line" lang="cpp"> <span class="n" style="color: #333333;">_String</span> <span class="p">(</span><span class="s" style="color: #dd1144;">"CLASSES"</span><span class="p">),</span> <span class="n" style="color: #333333;">_hyphyLFConstructCategoryMatrixClasses</span><span class="p">,</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="890" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
890
</td>
<td class="new_line diff-line-num old" data-linenumber="890" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC890" class="line" lang="cpp"> <span class="n" style="color: #333333;">_String</span> <span class="p">(</span><span class="s" style="color: #dd1144;">"SHORT"</span><span class="p">),</span> <span class="n" style="color: #333333;">_hyphyLFConstructCategoryMatrixClasses</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="891" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="890" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
890
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC890" class="line" lang="cpp"> <span class="n" style="color: #333333;">_String</span> <span class="p">(</span><span class="s" style="color: #dd1144;">"SHORT"</span><span class="p">),</span> <span class="n" style="color: #333333;">_hyphyLFConstructCategoryMatrixClasses</span><span class="p">,</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="891" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="891" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
891
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC891" class="line" lang="cpp"> <span class="n" style="color: #333333;">_String</span> <span class="p">(</span><span class="s" style="color: #dd1144;">"PARTITIONS"</span><span class="p">),</span> <span class="n" style="color: #333333;">_hyphyLFConstructCategoryMatrixPartitions</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="891" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
891
</td>
<td class="new_line diff-line-num" data-linenumber="892" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
892
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC892" class="line" lang="cpp"> <span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="892" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
892
</td>
<td class="new_line diff-line-num" data-linenumber="893" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
893
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC893" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="893" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
893
</td>
<td class="new_line diff-line-num" data-linenumber="894" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
894
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC894" class="line" lang="cpp"></span>
</pre></td>
</tr>
</table>
<br>
</li>
<li id="d09b45303442d6299978fa8d0c8f3338d6a17886">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/65547ade91167ae6589a244327500e8e1a4cf100#d09b45303442d6299978fa8d0c8f3338d6a17886"><strong style="font-weight: 600;">src/core/formula.cpp</strong></a>
<hr style="overflow: hidden; border: 1px solid #e1e1e1;">
<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#ffffff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="289" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="289" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -289,7 +289,7 @@ _StringBuffer const _Formula::toRPN (_hyFormulaStringConversionMode mode, _List*</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="289" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
289
</td>
<td class="new_line diff-line-num" data-linenumber="289" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
289
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC289" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">r</span><span class="p">;</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="290" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
290
</td>
<td class="new_line diff-line-num" data-linenumber="290" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
290
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC290" class="line" lang="cpp"><span class="p">}</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="291" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
291
</td>
<td class="new_line diff-line-num" data-linenumber="291" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
291
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC291" class="line" lang="cpp"><span class="c1" style="color: #999988; font-style: italic;">//__________________________________________________________________________________</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="292" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
292
</td>
<td class="new_line diff-line-num old" data-linenumber="292" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC292" class="line" lang="cpp"><span class="n" style="color: #333333;">BaseRef</span> <span class="n" style="color: #333333;">_Formula</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333333;">toStr</span> <span class="p">(</span><span class="n" style="color: #333333;">_hyFormulaStringConversionMode</span> <span class="n" style="color: #333333;">mode</span><span class="p">,</span> <span class="n" style="color: #333333;">_List</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">matched_names</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">bool</span> <span class="n" style="color: #333333;">drop_tree</span><span class="p">)</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="293" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="292" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
292
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC292" class="line" lang="cpp"><span class="n" style="color: #333333;">BaseRef</span> <span class="n" style="color: #333333;">_Formula</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333333;">toStr</span> <span class="p">(</span><span class="n" style="color: #333333;">_hyFormulaStringConversionMode</span> <span class="n" style="color: #333333;">mode</span><span class="p">,</span> <span class="n" style="color: #333333;">_List</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">matched_names</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">bool</span> <span class="n" style="color: #333333;">drop_tree</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">_StringBuffer</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">*</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">hbl_dependencies</span></span><span class="p">)</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="293" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
293
</td>
<td class="new_line diff-line-num" data-linenumber="293" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
293
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC293" class="line" lang="cpp"> <span class="n" style="color: #333333;">ConvertToTree</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="294" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
294
</td>
<td class="new_line diff-line-num" data-linenumber="294" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
294
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC294" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="295" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
295
</td>
<td class="new_line diff-line-num" data-linenumber="295" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
295
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC295" class="line" lang="cpp"> <span class="n" style="color: #333333;">_StringBuffer</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333333;">_StringBuffer</span> <span class="p">(</span><span class="mi" style="color: #009999;">64UL</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="297" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="297" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -297,8 +297,17 @@ BaseRef _Formula::toStr (_hyFormulaStringConversionMode mode, _List* matched_nam</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="297" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
297
</td>
<td class="new_line diff-line-num" data-linenumber="297" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
297
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC297" class="line" lang="cpp"> <span class="kt" style="color: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">savepd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">print_digit_specification</span><span class="p">;</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="298" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
298
</td>
<td class="new_line diff-line-num" data-linenumber="298" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
298
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC298" class="line" lang="cpp"> <span class="n" style="color: #333333;">print_digit_specification</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0L</span><span class="p">;</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="299" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
299
</td>
<td class="new_line diff-line-num" data-linenumber="299" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
299
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC299" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="300" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="300" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
300
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC300" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="300" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="301" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
301
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC301" class="line" lang="cpp"> </span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="300" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
300
</td>
<td class="new_line diff-line-num" data-linenumber="302" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
302
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC302" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">theTree</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #999988; font-style: italic;">// there is something to do</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="301" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
301
</td>
<td class="new_line diff-line-num old" data-linenumber="303" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC301" class="line" lang="cpp"> <span class="n" style="color: #333333;">SubtreeToString</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">result</span><span class="p">,</span> <span class="n" style="color: #333333;">theTree</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span><span class="p">,</span> <span class="n" style="color: #333333;">matched_names</span><span class="p">,</span> <span class="n" style="color: #333333;">nil</span><span class="p">,</span> <span class="n" style="color: #333333;">mode</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="302" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="303" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
303
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC303" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">hbl_dependencies</span><span class="p">)</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="302" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="304" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
304
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC304" class="line" lang="cpp"> <span class="n" style="color: #333333;">_SimpleList</span> <span class="n" style="color: #333333;">_tracker</span><span class="p">;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="302" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="305" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
305
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC305" class="line" lang="cpp"> <span class="n" style="color: #333333;">_AVLList</span> <span class="n" style="color: #333333;">tracker</span> <span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333333;">_tracker</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="302" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="306" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
306
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC306" class="line" lang="cpp"> <span class="n" style="color: #333333;">SubtreeToString</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">result</span><span class="p">,</span> <span class="n" style="color: #333333;">theTree</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span><span class="p">,</span> <span class="n" style="color: #333333;">matched_names</span><span class="p">,</span> <span class="n" style="color: #333333;">nil</span><span class="p">,</span> <span class="n" style="color: #333333;">mode</span><span class="p">,</span> <span class="n" style="color: #333333;">hbl_dependencies</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333333;">tracker</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="302" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="307" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
307
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC307" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="302" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="308" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
308
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC308" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="302" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="309" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
309
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC309" class="line" lang="cpp"> <span class="n" style="color: #333333;">SubtreeToString</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">result</span><span class="p">,</span> <span class="n" style="color: #333333;">theTree</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span><span class="p">,</span> <span class="n" style="color: #333333;">matched_names</span><span class="p">,</span> <span class="n" style="color: #333333;">nil</span><span class="p">,</span> <span class="n" style="color: #333333;">mode</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="302" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="310" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
310
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC310" class="line" lang="cpp"> <span class="p">}</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="302" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
302
</td>
<td class="new_line diff-line-num" data-linenumber="311" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
311
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC311" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="303" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
303
</td>
<td class="new_line diff-line-num" data-linenumber="312" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
312
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC312" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">theFormula</span><span class="p">.</span><span class="n" style="color: #333333;">countitems</span><span class="p">())</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="304" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
304
</td>
<td class="new_line diff-line-num" data-linenumber="313" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
313
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC313" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #dd1144;">"RPN:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333333;">toRPN</span> <span class="p">(</span><span class="n" style="color: #333333;">mode</span><span class="p">,</span> <span class="n" style="color: #333333;">matched_names</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="990" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="999" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -990,7 +999,7 @@ bool _Formula::InternalSimplify (node<long>* top_node) {</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="990" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
990
</td>
<td class="new_line diff-line-num" data-linenumber="999" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
999
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC999" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="991" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
991
</td>
<td class="new_line diff-line-num" data-linenumber="1000" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1000
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1000" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="992" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
992
</td>
<td class="new_line diff-line-num" data-linenumber="1001" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1001
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1001" class="line" lang="cpp"><span class="c1" style="color: #999988; font-style: italic;">//__________________________________________________________________________________</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="993" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
993
</td>
<td class="new_line diff-line-num old" data-linenumber="1002" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC993" class="line" lang="cpp"><span class="kt" style="color: #445588; font-weight: 600;">void</span> <span class="n" style="color: #333333;">_Formula</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333333;">SubtreeToString</span> <span class="p">(</span><span class="n" style="color: #333333;">_StringBuffer</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333333;">result</span><span class="p">,</span> <span class="n" style="color: #333333;">node</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #445588; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">>*</span> <span class="n" style="color: #333333;">top_node</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">op_level</span><span class="p">,</span> <span class="n" style="color: #333333;">_List</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">match_names</span><span class="p">,</span> <span class="n" style="color: #333333;">_Operation</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">this_node_op</span><span class="p">,</span> <span class="n" style="color: #333333;">_hyFormulaStringConversionMode</span> <span class="n" style="color: #333333;">mode</span><span class="p">)</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="994" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1002" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1002
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1002" class="line" lang="cpp"><span class="kt" style="color: #445588; font-weight: 600;">void</span> <span class="n" style="color: #333333;">_Formula</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333333;">SubtreeToString</span> <span class="p">(</span><span class="n" style="color: #333333;">_StringBuffer</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333333;">result</span><span class="p">,</span> <span class="n" style="color: #333333;">node</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #445588; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">>*</span> <span class="n" style="color: #333333;">top_node</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">op_level</span><span class="p">,</span> <span class="n" style="color: #333333;">_List</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">match_names</span><span class="p">,</span> <span class="n" style="color: #333333;">_Operation</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">this_node_op</span><span class="p">,</span> <span class="n" style="color: #333333;">_hyFormulaStringConversionMode</span> <span class="n" style="color: #333333;">mode</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">_StringBuffer</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">*</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">hbl_dependencies</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">_AVLList</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">*</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">hbl_tracker</span></span><span class="p">)</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="994" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
994
</td>
<td class="new_line diff-line-num" data-linenumber="1003" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1003
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1003" class="line" lang="cpp"> </span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="995" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
995
</td>
<td class="new_line diff-line-num" data-linenumber="1004" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1004
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1004" 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: #333333;">this_node_op</span><span class="p">)</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="996" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
996
</td>
<td class="new_line diff-line-num" data-linenumber="1005" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1005
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1005" 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: #333333;">top_node</span><span class="p">)</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1142" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1151" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1142,6 +1151,9 @@ void _Formula::SubtreeToString (_StringBuffer & result, node<long>* top_node, in</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1142" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1142
</td>
<td class="new_line diff-line-num" data-linenumber="1151" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1151
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">node_op_count</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #009999;">0L</span><span class="p">)</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1143" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1143
</td>
<td class="new_line diff-line-num" data-linenumber="1152" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1152
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1152" class="line" lang="cpp"> <span class="c1" style="color: #999988; font-style: italic;">// a user-defined function</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1144" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1144
</td>
<td class="new_line diff-line-num" data-linenumber="1153" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1153
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1153" class="line" lang="cpp"> <span class="kt" style="color: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">func_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">this_node_op</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">UserFunctionID</span><span class="p">();</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1145" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1154" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1154
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1154" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">hbl_dependencies</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333333;">hbl_tracker</span><span class="p">)</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1145" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1155" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1155
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1155" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">hbl_dependencies</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333333;">ExportBFFunction</span><span class="p">(</span><span class="n" style="color: #333333;">func_id</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="n" style="color: #333333;">hbl_tracker</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1145" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1156" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1156
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1156" class="line" lang="cpp"> <span class="p">}</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1145" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1145
</td>
<td class="new_line diff-line-num" data-linenumber="1157" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1157
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1157" class="line" lang="cpp"> <span class="n" style="color: #333333;">result</span><span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333333;">GetBFFunctionNameByIndex</span><span class="p">(</span><span class="n" style="color: #333333;">func_id</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1146" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1146
</td>
<td class="new_line diff-line-num" data-linenumber="1158" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1158
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1158" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">top_node</span><span class="p">)</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1147
</td>
<td class="new_line diff-line-num" data-linenumber="1159" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1159
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1159" class="line" lang="cpp"> <span class="n" style="color: #333333;">result</span><span class="o" style="font-weight: 600;"><<</span><span class="sc" style="color: #dd1144;">'('</span><span class="p">;</span></span>
</pre></td>
</tr>
</table>
<br>
</li>
<li id="07aceb8d215a75908cea626d9c80bc2a7c06639c">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/65547ade91167ae6589a244327500e8e1a4cf100#07aceb8d215a75908cea626d9c80bc2a7c06639c"><strong style="font-weight: 600;">src/core/global_things.cpp</strong></a>
<hr style="overflow: hidden; border: 1px solid #e1e1e1;">
<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#ffffff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -122,7 +122,7 @@ namespace hy_global {</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
122
</td>
<td class="new_line diff-line-num" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
122
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333333;">kErrorStringMatrixExportError</span> <span class="p">(</span><span class="s" style="color: #dd1144;">"Export matrix called with a non-polynomial matrix argument"</span><span class="p">),</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="123" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
123
</td>
<td class="new_line diff-line-num" data-linenumber="123" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
123
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333333;">kErrorStringNullOperand</span> <span class="p">(</span><span class="s" style="color: #dd1144;">"Attempting to operate on an undefined value; this is probably the result of an earlier 'soft' error condition"</span><span class="p">),</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="124" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
124
</td>
<td class="new_line diff-line-num" data-linenumber="124" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
124
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333333;">kErrorNumerical</span> <span class="p">(</span><span class="s" style="color: #dd1144;">"To treat numerical errors as warnings, please specify </span><span class="se" style="color: #dd1144;">\"</span><span class="s" style="color: #dd1144;">ENV=TOLERATE_NUMERICAL_ERRORS=1;</span><span class="se" style="color: #dd1144;">\"</span><span class="s" style="color: #dd1144;"> as the command line argument. This often resolves the issue, which is indicative of numerical instability."</span><span class="p">),</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
125
</td>
<td class="new_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333333;">kHyPhyVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">_String</span> <span class="p">(</span><span class="s" style="color: #dd1144;">"2.5.6<span class="idiff left right deletion" style="background-color: #fac5cd;">2</span>"</span><span class="p">),</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
125
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333333;">kHyPhyVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">_String</span> <span class="p">(</span><span class="s" style="color: #dd1144;">"2.5.6<span class="idiff left right addition" style="background-color: #c7f0d2;">3</span>"</span><span class="p">),</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="126" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
126
</td>
<td class="new_line diff-line-num" data-linenumber="126" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
126
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC126" class="line" lang="cpp"> </span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="127" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
127
</td>
<td class="new_line diff-line-num" data-linenumber="127" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
127
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333333;">kNoneToken</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #dd1144;">"None"</span><span class="p">,</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="128" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
128
</td>
<td class="new_line diff-line-num" data-linenumber="128" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
128
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333333;">kNullToken</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #dd1144;">"null"</span><span class="p">,</span></span>
</pre></td>
</tr>
</table>
<br>
</li>
<li id="46380d67c22541ee76ad7fa2f39c30110df90a7c">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/65547ade91167ae6589a244327500e8e1a4cf100#46380d67c22541ee76ad7fa2f39c30110df90a7c"><strong style="font-weight: 600;">src/core/include/batchlan.h</strong></a>
<hr style="overflow: hidden; border: 1px solid #e1e1e1;">
<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#ffffff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="644" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="644" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -644,7 +644,7 @@ _ExecutionList&</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="644" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
644
</td>
<td class="new_line diff-line-num" data-linenumber="644" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
644
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC644" class="line" lang="cpp"> <span class="n" style="color: #333333;">GetBFFunctionBody</span> <span class="p">(</span><span class="kt" style="color: #445588; font-weight: 600;">long</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="645" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
645
</td>
<td class="new_line diff-line-num" data-linenumber="645" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
645
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC645" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="646" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
646
</td>
<td class="new_line diff-line-num" data-linenumber="646" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
646
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC646" class="line" lang="cpp"><span class="n" style="color: #333333;">_String</span> <span class="k" style="font-weight: 600;">const</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="647" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
647
</td>
<td class="new_line diff-line-num old" data-linenumber="647" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC647" class="line" lang="cpp"> <span class="nf" style="color: #990000; font-weight: 600;">ExportBFFunction</span> <span class="p">(</span><span class="kt" style="color: #445588; font-weight: 600;">long</span><span class="p">,</span> <span class="kt" style="color: #445588; 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>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="648" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="647" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
647
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC647" class="line" lang="cpp"> <span class="nf" style="color: #990000; font-weight: 600;">ExportBFFunction</span> <span class="p">(</span><span class="kt" style="color: #445588; font-weight: 600;">long</span><span class="p">,</span> <span class="kt" style="color: #445588; 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 class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">_AVLList</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">*</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">nil</span></span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="648" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
648
</td>
<td class="new_line diff-line-num" data-linenumber="648" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
648
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC648" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="649" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
649
</td>
<td class="new_line diff-line-num" data-linenumber="649" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
649
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC649" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="650" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
650
</td>
<td class="new_line diff-line-num" data-linenumber="650" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
650
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC650" class="line" lang="cpp"><span class="kt" style="color: #445588; font-weight: 600;">void</span> <span class="nf" style="color: #990000; font-weight: 600;">ClearBFFunctionLists</span> <span class="p">(</span><span class="kt" style="color: #445588; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1L</span><span class="p">);</span></span>
</pre></td>
</tr>
</table>
<br>
</li>
<li id="40fc4f1e42852e6f2302e213cd9b3646abe98291">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/65547ade91167ae6589a244327500e8e1a4cf100#40fc4f1e42852e6f2302e213cd9b3646abe98291"><strong style="font-weight: 600;">src/core/include/formula.h</strong></a>
<hr style="overflow: hidden; border: 1px solid #e1e1e1;">
<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#ffffff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="149" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="149" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -149,7 +149,7 @@ public:</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="149" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
149
</td>
<td class="new_line diff-line-num" data-linenumber="149" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
149
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC149" class="line" lang="cpp"> <span class="kt" style="color: #445588; font-weight: 600;">void</span> <span class="n" style="color: #333333;">Duplicate</span> <span class="p">(</span><span class="n" style="color: #333333;">_Formula</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">bool</span> <span class="n" style="color: #333333;">deep_copy</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="150" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
150
</td>
<td class="new_line diff-line-num" data-linenumber="150" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
150
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC150" class="line" lang="cpp"> <span class="kt" style="color: #445588; font-weight: 600;">void</span> <span class="n" style="color: #333333;">DuplicateReference</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333333;">_Formula</span><span class="o" style="font-weight: 600;">*</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="151" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
151
</td>
<td class="new_line diff-line-num" data-linenumber="151" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
151
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC151" class="line" lang="cpp"> <span class="n" style="color: #333333;">BaseRef</span> <span class="n" style="color: #333333;">makeDynamic</span> <span class="p">(</span><span class="kt" style="color: #445588; font-weight: 600;">void</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="152" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
152
</td>
<td class="new_line diff-line-num old" data-linenumber="152" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333333;">BaseRef</span> <span class="n" style="color: #333333;">toStr</span> <span class="p">(</span><span class="n" style="color: #333333;">_hyFormulaStringConversionMode</span> <span class="n" style="color: #333333;">mode</span><span class="p">,</span> <span class="n" style="color: #333333;">_List</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">matchNames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">nil</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
152
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333333;">BaseRef</span> <span class="n" style="color: #333333;">toStr</span> <span class="p">(</span><span class="n" style="color: #333333;">_hyFormulaStringConversionMode</span> <span class="n" style="color: #333333;">mode</span><span class="p">,</span> <span class="n" style="color: #333333;">_List</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">matchNames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">nil</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">_StringBuffer</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">*</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">hbl_dependencies</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">nil</span></span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="153" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
153
</td>
<td class="new_line diff-line-num" data-linenumber="153" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
153
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC153" class="line" lang="cpp"> <span class="n" style="color: #333333;">_StringBuffer</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333333;">toRPN</span> <span class="p">(</span><span class="n" style="color: #333333;">_hyFormulaStringConversionMode</span> <span class="n" style="color: #333333;">mode</span><span class="p">,</span> <span class="n" style="color: #333333;">_List</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">matchNames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">nil</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="154" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
154
</td>
<td class="new_line diff-line-num" data-linenumber="154" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
154
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC154" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="155" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
155
</td>
<td class="new_line diff-line-num" data-linenumber="155" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
155
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC155" class="line" lang="cpp"> <span class="kt" style="color: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">ObjectClass</span> <span class="p">(</span><span class="kt" style="color: #445588; font-weight: 600;">void</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="288" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="288" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -288,7 +288,7 @@ public:</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="288" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
288
</td>
<td class="new_line diff-line-num" data-linenumber="288" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
288
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC288" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="289" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
289
</td>
<td class="new_line diff-line-num" data-linenumber="289" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
289
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC289" class="line" lang="cpp"><span class="k" style="font-weight: 600;">protected</span><span class="o" style="font-weight: 600;">:</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="290" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
290
</td>
<td class="new_line diff-line-num" data-linenumber="290" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
290
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC290" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="291" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
291
</td>
<td class="new_line diff-line-num old" data-linenumber="291" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC291" class="line" lang="cpp"> <span class="kt" style="color: #445588; font-weight: 600;">void</span> <span class="nf" style="color: #990000; font-weight: 600;">SubtreeToString</span> <span class="p">(</span><span class="n" style="color: #333333;">_StringBuffer</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333333;">result</span><span class="p">,</span> <span class="n" style="color: #333333;">node</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #445588; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">>*</span> <span class="n" style="color: #333333;">top_node</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">op_level</span><span class="p">,</span> <span class="n" style="color: #333333;">_List</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">match_names</span><span class="p">,</span> <span class="n" style="color: #333333;">_Operation</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">this_node_op</span><span class="p">,</span> <span class="n" style="color: #333333;">_hyFormulaStringConversionMode</span> <span class="n" style="color: #333333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">kFormulaStringConversionNormal</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="292" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="291" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
291
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC291" class="line" lang="cpp"> <span class="kt" style="color: #445588; font-weight: 600;">void</span> <span class="nf" style="color: #990000; font-weight: 600;">SubtreeToString</span> <span class="p">(</span><span class="n" style="color: #333333;">_StringBuffer</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333333;">result</span><span class="p">,</span> <span class="n" style="color: #333333;">node</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #445588; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">>*</span> <span class="n" style="color: #333333;">top_node</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">op_level</span><span class="p">,</span> <span class="n" style="color: #333333;">_List</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">match_names</span><span class="p">,</span> <span class="n" style="color: #333333;">_Operation</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">this_node_op</span><span class="p">,</span> <span class="n" style="color: #333333;">_hyFormulaStringConversionMode</span> <span class="n" style="color: #333333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">kFormulaStringConversionNormal</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">_StringBuffer</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">*</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">hbl_dependencies</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">nil</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">_AVLList</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">*</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">hbl_tracker</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">nil</span></span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="292" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
292
</td>
<td class="new_line diff-line-num" data-linenumber="292" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
292
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC292" class="line" lang="cpp"> <span class="kt" style="color: #445588; font-weight: 600;">void</span> <span class="nf" style="color: #990000; font-weight: 600;">ConvertToTree</span> <span class="p">(</span><span class="kt" style="color: #445588; font-weight: 600;">bool</span> <span class="n" style="color: #333333;">err_msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="293" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
293
</td>
<td class="new_line diff-line-num" data-linenumber="293" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
293
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC293" class="line" lang="cpp"> <span class="kt" style="color: #445588; font-weight: 600;">void</span> <span class="nf" style="color: #990000; font-weight: 600;">ConvertFromTree</span> <span class="p">(</span><span class="kt" style="color: #445588; font-weight: 600;">void</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="294" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
294
</td>
<td class="new_line diff-line-num" data-linenumber="294" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
294
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC294" class="line" lang="cpp"> <span class="kt" style="color: #445588; font-weight: 600;">bool</span> <span class="nf" style="color: #990000; font-weight: 600;">CheckSimpleTerm</span> <span class="p">(</span><span class="n" style="color: #333333;">HBLObjectRef</span><span class="p">);</span></span>
</pre></td>
</tr>
</table>
<br>
</li>
<li id="7277ab70f1a79733638d6141d1cb1d3f8b9c26c2">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/65547ade91167ae6589a244327500e8e1a4cf100#7277ab70f1a79733638d6141d1cb1d3f8b9c26c2"><strong style="font-weight: 600;">src/core/include/likefunc.h</strong></a>
<hr style="overflow: hidden; border: 1px solid #e1e1e1;">
<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#ffffff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="74" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="74" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -74,6 +74,8 @@ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="74" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
74
</td>
<td class="new_line diff-line-num" data-linenumber="74" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
74
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC74" class="line" lang="cpp"><span class="cp" style="color: #999999; font-weight: 600;">#define _hyphyLFConstructCategoryMatrixWeights 2</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
75
</td>
<td class="new_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
75
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC75" class="line" lang="cpp"><span class="cp" style="color: #999999; font-weight: 600;">#define _hyphyLFConstructCategoryMatrixPosteriors 3</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
76
</td>
<td class="new_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
76
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC76" class="line" lang="cpp"><span class="cp" style="color: #999999; font-weight: 600;">#define _hyphyLFConstructCategoryMatrixSiteProbabilities 4</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
77
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC77" class="line" lang="cpp"><span class="cp" style="color: #999999; font-weight: 600;">#define _hyphyLFConstructCategoryMatrixPartitions 5</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
78
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC78" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
77
</td>
<td class="new_line diff-line-num" data-linenumber="79" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
79
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC79" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="78" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
78
</td>
<td class="new_line diff-line-num" data-linenumber="80" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
80
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC80" class="line" lang="cpp"><span class="cm" style="color: #999988; font-style: italic;">/* likelihood seialization model */</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="79" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
79
</td>
<td class="new_line diff-line-num" data-linenumber="81" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
81
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC81" class="line" lang="cpp"></span>
</pre></td>
</tr>
</table>
<br>
</li>
<li id="2a8dd324ded753b0b3c559ac3950a2881ccd7a93">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/65547ade91167ae6589a244327500e8e1a4cf100#2a8dd324ded753b0b3c559ac3950a2881ccd7a93"><strong style="font-weight: 600;">src/core/likefunc.cpp</strong></a>
<hr style="overflow: hidden; border: 1px solid #e1e1e1;">
<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#ffffff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1563" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1563" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1563,6 +1563,15 @@ _Matrix* _LikelihoodFunction::ConstructCategoryMatrix (const _SimpleList& whi</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1563" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1563
</td>
<td class="new_line diff-line-num" data-linenumber="1563" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1563
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1563" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1564" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1564
</td>
<td class="new_line diff-line-num" data-linenumber="1564" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1564
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1564" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1565" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1565
</td>
<td class="new_line diff-line-num" data-linenumber="1565" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1565
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1565" class="line" lang="cpp"> <span class="n" style="color: #333333;">PrepareToCompute</span><span class="p">();</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1566" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1566" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1566
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1566" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">runMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333333;">_hyphyLFConstructCategoryMatrixPartitions</span><span class="p">)</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1566" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1567" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1567
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1567" class="line" lang="cpp"> <span class="n" style="color: #333333;">_Matrix</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">block_likelihoods</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333333;">_Matrix</span> <span class="p">(</span><span class="mi" style="color: #009999;">1</span><span class="p">,</span> <span class="n" style="color: #333333;">whichParts</span><span class="p">.</span><span class="n" style="color: #333333;">lLength</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1566" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1568" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1568
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1568" class="line" lang="cpp"> <span class="n" style="color: #333333;">whichParts</span><span class="p">.</span><span class="n" style="color: #333333;">Each</span><span class="p">([</span><span class="k" style="font-weight: 600;">this</span><span class="p">,</span> <span class="n" style="color: #333333;">block_likelihoods</span><span class="p">]</span> <span class="p">(</span><span class="kt" style="color: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">item</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">unsigned</span> <span class="kt" style="color: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">i</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="kt" style="color: #445588; font-weight: 600;">void</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1566" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1569" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1569
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1569" class="line" lang="cpp"> <span class="n" style="color: #333333;">block_likelihoods</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">Store</span> <span class="p">(</span><span class="mi" style="color: #009999;">0</span><span class="p">,</span> <span class="n" style="color: #333333;">i</span><span class="p">,</span> <span class="n" style="color: #333333;">ComputeBlock</span><span class="p">(</span><span class="n" style="color: #333333;">item</span><span class="p">));</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1566" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1570" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1570
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1570" class="line" lang="cpp"> <span class="p">});</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1566" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1571" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1571
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1571" class="line" lang="cpp"> <span class="n" style="color: #333333;">DoneComputing</span><span class="p">();</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1566" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1572" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1572
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1572" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">block_likelihoods</span><span class="p">;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1566" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1573" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1573
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1573" class="line" lang="cpp"> <span class="p">}</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1566" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1574" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1574
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1574" class="line" lang="cpp"> </span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1566" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1566
</td>
<td class="new_line diff-line-num" data-linenumber="1575" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1575
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1575" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">runMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333333;">_hyphyLFConstructCategoryMatrixConditionals</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333333;">runMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333333;">_hyphyLFConstructCategoryMatrixWeights</span><span class="p">)</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1567" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1567
</td>
<td class="new_line diff-line-num" data-linenumber="1576" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1576
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1576" class="line" lang="cpp"> <span class="c1" style="color: #999988; font-style: italic;">// just return the matrix with class weights</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1568" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1568
</td>
<td class="new_line diff-line-num" data-linenumber="1577" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1577
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1577" class="line" lang="cpp"> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1608" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1617" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1608,9 +1617,8 @@ _Matrix* _LikelihoodFunction::ConstructCategoryMatrix (const _SimpleList& whi</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1608" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1608
</td>
<td class="new_line diff-line-num" data-linenumber="1617" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1617
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1617" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1609" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1609
</td>
<td class="new_line diff-line-num" data-linenumber="1618" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1618
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1618" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1610" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1610
</td>
<td class="new_line diff-line-num" data-linenumber="1619" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1619
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1619" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1611" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1611
</td>
<td class="new_line diff-line-num old" data-linenumber="1620" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1611" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">runMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333333;">_hyphyLFConstructCategoryMatrixClasses</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333333;">runMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333333;">_hyphyLFConstructCategoryMatrixSiteProbabilities</span><span class="p">)</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1612" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1620" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1620
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1620" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">runMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333333;">_hyphyLFConstructCategoryMatrixClasses</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333333;">runMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333333;">_hyphyLFConstructCategoryMatrixSiteProbabilities</span><span class="p">)</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">{</span></span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1612" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1612
</td>
<td class="new_line diff-line-num" data-linenumber="1621" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1621
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1621" class="line" lang="cpp"> <span class="c1" style="color: #999988; font-style: italic;">// just return the maximum conditional likelihood category</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1613" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1613
</td>
<td class="new_line diff-line-num old" data-linenumber="1622" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1613" class="line" lang="cpp"> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1614" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1614
</td>
<td class="new_line diff-line-num" data-linenumber="1622" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1622
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1622" class="line" lang="cpp"> <span class="n" style="color: #333333;">_Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333333;">_Matrix</span> <span class="p">(</span><span class="n" style="color: #333333;">hDim</span><span class="p">,</span><span class="n" style="color: #333333;">vDim</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">),</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1615" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1615
</td>
<td class="new_line diff-line-num" data-linenumber="1623" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1623
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1623" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">cache</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">nil</span><span class="p">;</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1616" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1616
</td>
<td class="new_line diff-line-num" data-linenumber="1624" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1624
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1624" class="line" lang="cpp"> <span class="n" style="color: #333333;">_SimpleList</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">scalerCache</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">nil</span><span class="p">;</span></span>
</pre></td>
</tr>
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10110" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10118" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -10110,6 +10118,22 @@ void _LikelihoodFunction::SerializeLF(_StringBuffer & rec, char opt,</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10110" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10110
</td>
<td class="new_line diff-line-num" data-linenumber="10118" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10118
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10118" class="line" lang="cpp"> <span class="n" style="color: #333333;">rec</span><span class="p">.</span><span class="n" style="color: #333333;">AppendAnAssignmentToBuffer</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333333;">hy_env</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333333;">assume_reversible</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #990000; font-weight: 600;">_String</span><span class="p">(</span><span class="n" style="color: #333333;">hy_env</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333333;">EnvVariableGetNumber</span><span class="p">(</span><span class="n" style="color: #333333;">hy_env</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333333;">assume_reversible</span><span class="p">,</span> <span class="mf" style="color: #009999;">0.</span><span class="p">)));</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10111" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10111
</td>
<td class="new_line diff-line-num" data-linenumber="10119" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10119
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10119" class="line" lang="cpp"> <span class="n" style="color: #333333;">rec</span><span class="p">.</span><span class="n" style="color: #333333;">AppendAnAssignmentToBuffer</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333333;">kUseLastResults</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #990000; font-weight: 600;">_String</span><span class="p">(</span><span class="n" style="color: #333333;">hy_env</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333333;">EnvVariableGetNumber</span><span class="p">(</span><span class="n" style="color: #333333;">kUseLastResults</span><span class="p">,</span> <span class="mf" style="color: #009999;">0.</span><span class="p">)));</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10112" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10112
</td>
<td class="new_line diff-line-num" data-linenumber="10120" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10120
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10120" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10121" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10121
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10121" class="line" lang="cpp"> <span class="cm" style="color: #999988; font-style: italic;">/** 20241022 SLKP</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10122
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10122" class="line" lang="cpp"><span class="cm" style="color: #999988; font-style: italic;"> if there's a computing template defined, we need to export HBL functions that in may be referencing</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10123" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10123
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10123" class="line" lang="cpp"><span class="cm" style="color: #999988; font-style: italic;"> */</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10124" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10124
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10124" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10125" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10125
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10125" class="line" lang="cpp"> <span class="n" style="color: #333333;">_StringBuffer</span> <span class="n" style="color: #333333;">exported_compute_template</span><span class="p">,</span> <span class="n" style="color: #333333;">template_code</span><span class="p">;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10126" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10126
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10126" class="line" lang="cpp"> </span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10127" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10127
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10127" class="line" lang="cpp"> </span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10128" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10128
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10128" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">computingTemplate</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333333;">templateKind</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333333;">_hyphyLFComputationalTemplateNone</span><span class="p">)</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10129" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10129
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10129" class="line" lang="cpp"> </span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10130" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10130
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10130" class="line" lang="cpp"> <span class="n" style="color: #333333;">template_code</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #dd1144;">",</span><span class="se" style="color: #dd1144;">\"</span><span class="s" style="color: #dd1144;">"</span><span class="p">;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10131" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10131
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10131" class="line" lang="cpp"> <span class="n" style="color: #333333;">template_code</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333333;">_String</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333333;">computingTemplate</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">toStr</span><span class="p">(</span><span class="n" style="color: #333333;">kFormulaStringConversionNormal</span><span class="p">,</span> <span class="n" style="color: #333333;">nil</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333333;">exported_compute_template</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10132" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10132
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10132" class="line" lang="cpp"> <span class="n" style="color: #333333;">template_code</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #dd1144;">'"'</span><span class="p">;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10133" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10133
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10133" class="line" lang="cpp"> <span class="p">}</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10134" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10134
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10134" class="line" lang="cpp"> </span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10135" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10135
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10135" class="line" lang="cpp"> <span class="n" style="color: #333333;">rec</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333333;">exported_compute_template</span><span class="p">;</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10136" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10136
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10136" class="line" lang="cpp"> </span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10113
</td>
<td class="new_line diff-line-num" data-linenumber="10137" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10137
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10137" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">frequencyVectors</span><span class="p">.</span><span class="n" style="color: #333333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10114" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10114
</td>
<td class="new_line diff-line-num" data-linenumber="10138" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10138
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10138" class="line" lang="cpp"> <span class="n" style="color: #333333;">rec</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #dd1144;">"LikelihoodFunction "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">lfName</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #dd1144;">" = ("</span><span class="p">;</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10115" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10115
</td>
<td class="new_line diff-line-num" data-linenumber="10139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10139
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10139" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10124" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10148" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -10124,6 +10148,7 @@ void _LikelihoodFunction::SerializeLF(_StringBuffer & rec, char opt,</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10124" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10124
</td>
<td class="new_line diff-line-num" data-linenumber="10148" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10148
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10148" class="line" lang="cpp"> <span class="n" style="color: #333333;">rec</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">GetFilterName</span><span class="p">(</span><span class="n" style="color: #333333;">redirector</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">get</span><span class="p">(</span><span class="n" style="color: #333333;">idx</span><span class="p">))</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #dd1144;">','</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">LocateVar</span><span class="p">(</span><span class="n" style="color: #333333;">redirectorT</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">list_data</span><span class="p">[</span><span class="n" style="color: #333333;">idx</span><span class="p">])</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">GetName</span><span class="p">();</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10125" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10125
</td>
<td class="new_line diff-line-num" data-linenumber="10149" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10149
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10149" class="line" lang="cpp"> <span class="p">}</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10126" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10126
</td>
<td class="new_line diff-line-num" data-linenumber="10150" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10150
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10150" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10127" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10151" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10151
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10151" class="line" lang="cpp"> </span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10127" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10127
</td>
<td class="new_line diff-line-num" data-linenumber="10152" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10152
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10152" class="line" lang="cpp"> <span class="n" style="color: #333333;">rec</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #dd1144;">"LikelihoodFunction3 "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">lfName</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #dd1144;">" = ("</span><span class="p">;</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10128" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10128
</td>
<td class="new_line diff-line-num" data-linenumber="10153" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10153
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10153" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10129" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10129
</td>
<td class="new_line diff-line-num" data-linenumber="10154" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10154
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10154" class="line" lang="cpp"> <span class="kt" style="color: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">dsID</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="p">;</span></span>
</pre></td>
</tr>
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10137" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10162" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -10137,11 +10162,7 @@ void _LikelihoodFunction::SerializeLF(_StringBuffer & rec, char opt,</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10137" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10137
</td>
<td class="new_line diff-line-num" data-linenumber="10162" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10162
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10162" class="line" lang="cpp"> <span class="p">}</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10138" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10138
</td>
<td class="new_line diff-line-num" data-linenumber="10163" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10163
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10163" class="line" lang="cpp"> <span class="p">}</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10139
</td>
<td class="new_line diff-line-num" data-linenumber="10164" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10164
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10164" class="line" lang="cpp"> </span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="10140" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
10140
</td>
<td class="new_line diff-line-num old" data-linenumber="10165" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10140" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">computingTemplate</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333333;">templateKind</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">1</span><span class="p">)</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="10141" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
10141
</td>
<td class="new_line diff-line-num old" data-linenumber="10165" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10141" class="line" lang="cpp"> <span class="n" style="color: #333333;">rec</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #dd1144;">",</span><span class="se" style="color: #dd1144;">\"</span><span class="s" style="color: #dd1144;">"</span><span class="p">;</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="10142" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
10142
</td>
<td class="new_line diff-line-num old" data-linenumber="10165" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10142" class="line" lang="cpp"> <span class="n" style="color: #333333;">rec</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333333;">_String</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333333;">computingTemplate</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">toStr</span><span class="p">(</span><span class="n" style="color: #333333;">kFormulaStringConversionNormal</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="10143" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
10143
</td>
<td class="new_line diff-line-num old" data-linenumber="10165" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10143" class="line" lang="cpp"> <span class="n" style="color: #333333;">rec</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #dd1144;">'"'</span><span class="p">;</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="10144" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
10144
</td>
<td class="new_line diff-line-num old" data-linenumber="10165" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10144" class="line" lang="cpp"> <span class="p">}</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10145" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10165" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10165
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10165" class="line" lang="cpp"> <span class="n" style="color: #333333;">rec</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333333;">template_code</span><span class="p">;</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10145" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10145
</td>
<td class="new_line diff-line-num" data-linenumber="10166" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10166
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10166" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10146" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10146
</td>
<td class="new_line diff-line-num" data-linenumber="10167" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10167
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10167" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">opt</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333333;">_hyphyLFSerializeModeOptimize</span><span class="p">)</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10147
</td>
<td class="new_line diff-line-num" data-linenumber="10168" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10168
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10168" class="line" lang="cpp"> <span class="n" style="color: #333333;">rec</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #dd1144;">");</span><span class="se" style="color: #dd1144;">\n</span><span class="s" style="color: #dd1144;">"</span><span class="p">;</span></span>
</pre></td>
</tr>
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10201" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10222" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -10201,11 +10222,12 @@ void _LikelihoodFunction::SerializeLF(_StringBuffer & rec, char opt,</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10201" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10201
</td>
<td class="new_line diff-line-num" data-linenumber="10222" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10222
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10222" class="line" lang="cpp"><span class="c1" style="color: #999988; font-style: italic;">//_______________________________________________________________________________________</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10202" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10202
</td>
<td class="new_line diff-line-num" data-linenumber="10223" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10223
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10223" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10203" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10203
</td>
<td class="new_line diff-line-num" data-linenumber="10224" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10224
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10224" class="line" lang="cpp"><span class="n" style="color: #333333;">BaseRef</span> <span class="n" style="color: #333333;">_LikelihoodFunction</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333333;">toStr</span> <span class="p">(</span><span class="kt" style="color: #445588; font-weight: 600;">unsigned</span> <span class="kt" style="color: #445588; font-weight: 600;">long</span><span class="p">)</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="10204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
10204
</td>
<td class="new_line diff-line-num old" data-linenumber="10225" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10204" class="line" lang="cpp"> <span class="n" style="color: #333333;">hyFloat</span> <span class="n" style="color: #333333;">longOrShort</span><span class="p">,</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10205" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10225" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10225
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10225" class="line" lang="cpp"> </span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10205" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10226" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10226
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10226" class="line" lang="cpp"> <span class="n" style="color: #333333;">hyFloat</span> <span class="n" style="color: #333333;">longOrShort</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">hy_env</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333333;">EnvVariableGetNumber</span> <span class="p">(</span><span class="n" style="color: #333333;">likefuncOutput</span><span class="p">,</span> <span class="mf" style="color: #009999;">2.0</span><span class="p">),</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10205" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10205
</td>
<td class="new_line diff-line-num" data-linenumber="10227" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10227
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10227" class="line" lang="cpp"> <span class="n" style="color: #333333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #009999;">0.0</span><span class="p">;</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10206" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10206
</td>
<td class="new_line diff-line-num" data-linenumber="10228" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10228
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10228" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="10207" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
10207
</td>
<td class="new_line diff-line-num old" data-linenumber="10229" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10207" class="line" lang="cpp"> <span class="n" style="color: #333333;"><span class="idiff left deletion" style="background-color: #fac5cd;">checkParameter</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">(</span></span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">likefuncOutput</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">longOrShort</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="mf" style="color: #009999;"><span class="idiff deletion" style="background-color: #fac5cd;">2.0</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">);</span></span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="10208" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
10208
</td>
<td class="new_line diff-line-num old" data-linenumber="10229" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10208" class="line" lang="cpp"></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10209" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10229" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10229
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10229" class="line" lang="cpp"> </span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10209" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10230" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10230
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10230" class="line" lang="cpp"> </span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10209" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10209
</td>
<td class="new_line diff-line-num" data-linenumber="10231" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10231
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10231" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">longOrShort</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #009999;">4.0</span><span class="p">)</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10210" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10210
</td>
<td class="new_line diff-line-num" data-linenumber="10232" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10232
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10232" class="line" lang="cpp"> <span class="n" style="color: #333333;">PrepareToCompute</span><span class="p">();</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10211" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10211
</td>
<td class="new_line diff-line-num" data-linenumber="10233" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10233
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10233" class="line" lang="cpp"> <span class="n" style="color: #333333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">Compute</span><span class="p">();</span></span>
</pre></td>
</tr>
<tr class="line_holder match" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10403" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10425" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -10403,7 +10425,7 @@ BaseRef _LikelihoodFunction::toStr (unsigned long) {</td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10403" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10403
</td>
<td class="new_line diff-line-num" data-linenumber="10425" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10425
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10425" class="line" lang="cpp"> <span class="n" style="color: #333333;">_Variable</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">GetIthDependentVar</span><span class="p">(</span><span class="n" style="color: #333333;">i</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10404" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10404
</td>
<td class="new_line diff-line-num" data-linenumber="10426" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10426
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10426" class="line" lang="cpp"> <span class="n" style="color: #333333;">_String</span> <span class="n" style="color: #333333;">value</span> <span class="p">((</span><span class="n" style="color: #333333;">_String</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333333;">v</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">GetFormulaString</span><span class="p">(</span><span class="n" style="color: #333333;">kFormulaStringConversionNormal</span><span class="p">),</span> <span class="n" style="color: #333333;">kAppendAnAssignmentToBufferPlain</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10405" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10405
</td>
<td class="new_line diff-line-num" data-linenumber="10427" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10427
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10427" class="line" lang="cpp"> <span class="n" style="color: #333333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">value</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #dd1144;">" = "</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333333;">_String</span> <span class="p">((</span><span class="n" style="color: #333333;">_String</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333333;">v</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">toStr</span><span class="p">());</span></span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="10406" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
10406
</td>
<td class="new_line diff-line-num old" data-linenumber="10428" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10406" class="line" lang="cpp"> <span class="n" style="color: #333333;">res</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">AppendAnAssignmentToBuffer</span><span class="p">(</span><span class="n" style="color: #333333;">GetIthDependentName</span><span class="p">(</span><span class="n" style="color: #333333;">i</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333333;">value</span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10407" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="10428" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10428
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10428" class="line" lang="cpp"> <span class="n" style="color: #333333;">res</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">AppendAnAssignmentToBuffer</span><span class="p">(</span><span class="n" style="color: #333333;">GetIthDependentName</span><span class="p">(</span><span class="n" style="color: #333333;">i</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333333;">value</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">kAppendAnAssignmentToBufferPlain</span></span><span class="p">);</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10407" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10407
</td>
<td class="new_line diff-line-num" data-linenumber="10429" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10429
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10429" class="line" lang="cpp"> <span class="p">}</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10408" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10408
</td>
<td class="new_line diff-line-num" data-linenumber="10430" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10430
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10430" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
</pre></td>
</tr>
<tr class="line_holder" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10409" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10409
</td>
<td class="new_line diff-line-num" data-linenumber="10431" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10431
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10431" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">res</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333333;">_String</span> <span class="p">(</span><span class="n" style="color: #333333;">value</span><span class="p">,</span> <span class="s" style="color: #dd1144;">"%15.15g"</span><span class="p">);</span></span>
</pre></td>
</tr>
</table>
<br>
</li>
</div>
<div class="footer" style="margin-top: 10px;">
<p style="font-size: small; color: #737278;">
—
<br>
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/65547ade91167ae6589a244327500e8e1a4cf100">View it on GitLab</a>.
<br>
You're receiving this email because of your account on <a target="_blank" rel="noopener noreferrer" href="https://salsa.debian.org">salsa.debian.org</a>. <a href="https://salsa.debian.org/-/profile/notifications" target="_blank" rel="noopener noreferrer" class="mng-notif-link">Manage all notifications</a> · <a href="https://salsa.debian.org/help" target="_blank" rel="noopener noreferrer" class="help-link">Help</a>
<script type="application/ld+json">{"@context":"http://schema.org","@type":"EmailMessage","action":{"@type":"ViewAction","name":"View Commit","url":"https://salsa.debian.org/med-team/hyphy/-/commit/65547ade91167ae6589a244327500e8e1a4cf100"}}</script>
</p>
</div>
</body>
</html>