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<h3 style="margin-top: 20px; margin-bottom: 10px;">
Étienne Mollier pushed to branch master at <a href="https://salsa.debian.org/med-team/hyphy">Debian Med / hyphy</a>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
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<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/hyphy/-/commit/62b8190b71685492a2d15f7cbd212d3a3b80bf45">62b8190b</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2025-02-15T19:18:01+01:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu 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 2.5.68+dfsg</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/hyphy/-/commit/0e834a3cd1ed9b93cba583f2e1ccff88347a7305">0e834a3c</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2025-02-15T19:18:09+01:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu 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;'>Update upstream source from tag 'upstream/2.5.68+dfsg'
Update to upstream version '2.5.68+dfsg'
with Debian dir 2d55b8548b232c5481d02174ef0eaaf23ada1e4f</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/hyphy/-/commit/0fd4fec08edb43e6237f22231baa0249d55c4229">0fd4fec0</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2025-02-15T19:19:23+01:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu 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;'>d/patches/*: unfuzz all patches.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/hyphy/-/commit/cab2836da06a67c36d4d8e44d103577abde69da1">cab2836d</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2025-02-15T19:25:32+01:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu 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;'>d/changelog: ready for upload to unstable.
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
30 changed files:
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<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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Dockerfile
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<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#63c3307a25f0c1334b59e145f9fc809c05bbfa70">
debian/patches/rm_arch_specific_flags.patch
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<a href="#fae4045e7c53be7e233f4d504a872eab7bffa150">
debian/patches/set-zlib-after-setting-default-libs.patch
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<a href="#d185b62d54557160e7ddc743405a9cec66dcaa96">
debian/patches/use_debian_sqlite.patch
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res/TemplateBatchFiles/F_ST.bf
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<a href="#817efc81f1180519a6136b50a447433f20cf679d">
res/TemplateBatchFiles/SelectionAnalyses/FEL.bf
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<a href="#bc98d7300147ce39ef8ee0f9b35f3252bebd01d2">
res/TemplateBatchFiles/SelectionAnalyses/MEME.bf
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<a href="#cf5243a3058ebeab74574f8cd2c771cd63a43208">
res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf
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res/TemplateBatchFiles/libv3/models/frequencies.bf
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res/TemplateBatchFiles/libv3/models/parameters.bf
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res/TemplateBatchFiles/libv3/tasks/estimators.bf
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src/core/fisher_exact.cpp
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src/core/global_things.cpp
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src/core/likefunc.cpp
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src/core/likefunc2.cpp
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<a href="#81843dd3cf849d08e0f197d837dd373534c7c756">
src/core/matrix.cpp
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src/core/tree_evaluator.cpp
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tests/hbltests/libv3/FEL.wbf
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tests/hbltests/libv3/MEME.wbf
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tests/hbltests/libv3/algae-mtDNA.wbf
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
Changes:
</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong style="font-weight: 600;">CMakeLists.txt</strong></a>
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<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">
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -7,6 +7,7 @@ enable_testing()</td>
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<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
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"></span>
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<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
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CONFIGURATION_TYPES Release<span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
9
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"></span>
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<td class="old_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">
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"></span>
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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"><span class="c1" style="color: #999988; font-style: italic;">#-------------------------------------------------------------------------------</span></span>
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11
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"><span class="c1" style="color: #999988; font-style: italic;"># OPTIONS</span></span>
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<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">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"><span class="c1" style="color: #999988; font-style: italic;">#-------------------------------------------------------------------------------</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="170" style="width: 35px; 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="171" style="width: 35px; 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">@@ -170,12 +171,14 @@ set_source_files_properties(${SRC_CORE} ${SRC_NEW} {SRC_UTILS} PROPERTIES COMPIL</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"></span>
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<td class="old_line diff-line-num" data-linenumber="171" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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172
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>DEFAULT_WARNING_FLAGS <span class="s2" style="color: #dd1144;">" -w -Weffc++ -Wextra -Wall "</span><span class="p">)</span></span>
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<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
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<td class="new_line diff-line-num" data-linenumber="173" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
173
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>DEFAULT_DEBUG_WARNING_FLAGS <span class="s2" style="color: #dd1144;">"-Wall -Wno-int-to-pointer-cast -Wno-conversion-null -Wno-sign-compare"</span><span class="p">)</span></span>
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173
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<td class="new_line diff-line-num old" data-linenumber="174" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>ADDITIONAL_FLAGS <span class="s2" style="color: #dd1144;">""</span><span class="p">)</span></span>
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<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">
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>ADDITIONAL_FLAGS <span class="s2" style="color: #dd1144;">"<span class="idiff left right addition" style="background-color: #c7f0d2;">-g</span>"</span><span class="p">)</span></span>
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<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
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<td class="new_line diff-line-num" data-linenumber="175" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
175
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"></span>
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<td class="old_line diff-line-num" data-linenumber="175" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
175
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<td class="new_line diff-line-num" data-linenumber="176" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
176
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>DEBUGFLAGS<span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="176" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
176
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<td class="new_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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>ADDITIONAL_FLAGS <span class="s2" style="color: #dd1144;">"-g"</span><span class="p">)</span></span>
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<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
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<td class="new_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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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<td class="old_line diff-line-num" data-linenumber="178" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
178
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<td class="new_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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"></span>
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<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">
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<td class="new_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
180
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"><span class="c1" style="color: #999988; font-style: italic;">#include_directories("/Library/Developer/CommandLineTools/SDKs/MacOSX15.2.sdk/usr/include/c++/v1")</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"></span>
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179
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"></span>
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180
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX<span class="p">)</span></span>
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181
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<td class="new_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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"> <span class="nb" style="color: #0086b3;">execute_process</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="371" style="width: 35px; 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="374" style="width: 35px; 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">@@ -371,6 +374,7 @@ endif(NOT NOZLIB)</td>
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371
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374
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC374" class="line" lang="cmake"></span>
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372
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375
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC375" class="line" lang="cmake"></span>
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373
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376
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC376" class="line" lang="cmake"></span>
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377
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC377" class="line" lang="cmake"></span>
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374
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<td class="new_line diff-line-num" data-linenumber="378" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
378
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC378" class="line" lang="cmake"><span class="c1" style="color: #999988; font-style: italic;">#-------------------------------------------------------------------------------</span></span>
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375
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379
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376
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380
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -678,10 +682,12 @@ makeLink(HYPHYMP hyphy hyphy)</td>
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678
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682
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC682" class="line" lang="cmake"><span class="c1" style="color: #999988; font-style: italic;"># TESTS</span></span>
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679
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683
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC683" class="line" lang="cmake"><span class="c1" style="color: #999988; font-style: italic;">#-------------------------------------------------------------------------------</span></span>
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680
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684
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC684" class="line" lang="cmake"></span>
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<td class="old_line diff-line-num new" data-linenumber="681" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="685" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
685
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC685" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>HYPHY_ENV_ARG <span class="s2" style="color: #dd1144;">"ENV=TOLERATE_NUMERICAL_ERRORS=1;"</span><span class="p">)</span></span>
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686
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC686" class="line" lang="cmake"></span>
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681
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<td class="new_line diff-line-num" data-linenumber="687" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
687
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC687" class="line" lang="cmake"></span>
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<td class="old_line diff-line-num" data-linenumber="682" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
682
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<td class="new_line diff-line-num" data-linenumber="688" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
688
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC688" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>NAME UNIT-TESTS COMMAND bash run_unit_tests.sh<span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="683" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
683
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<td class="new_line diff-line-num" data-linenumber="689" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
689
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC689" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>CODON HYPHYMP tests/hbltests/SimpleOptimizations/SmallCodon.bf<span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="684" 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">
684
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<td class="new_line diff-line-num old" data-linenumber="690" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC684" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>PROTEIN HYPHYMP <span class="idiff left right deletion" style="background-color: #fac5cd;">CPU=1 </span>tests/hbltests/SimpleOptimizations/IntermediateProtein.bf<span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="690" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
690
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC690" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>PROTEIN HYPHYMP tests/hbltests/SimpleOptimizations/IntermediateProtein.bf<span class="p">)</span></span>
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685
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<td class="new_line diff-line-num" data-linenumber="691" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
691
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC691" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>MTCODON HYPHYMP tests/hbltests/libv3/mtDNA-code.wbf<span class="p">)</span></span>
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686
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<td class="new_line diff-line-num" data-linenumber="692" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
692
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC692" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>ALGAE HYPHYMP tests/hbltests/libv3/algae-mtDNA.wbf<span class="p">)</span></span>
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687
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<td class="new_line diff-line-num" data-linenumber="693" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
693
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC693" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>CILIATES HYPHYMP tests/hbltests/libv3/ciliate-code.wbf<span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="697" style="width: 35px; 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="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="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -697,8 +703,12 @@ add_test (RELAX HYPHYMP tests/hbltests/libv3/RELAX.wbf)</td>
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697
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<td class="new_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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC703" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>FUBAR HYPHYMP tests/hbltests/libv3/FUBAR.wbf<span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="698" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
698
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<td class="new_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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC704" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>BGM HYPHYMP tests/hbltests/libv3/BGM.wbf<span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="699" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
699
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<td class="new_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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC705" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>CONTRAST-FEL HYPHYMP tests/hbltests/libv3/CFEL.wbf<span class="p">)</span></span>
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700
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<td class="new_line diff-line-num old" data-linenumber="706" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC700" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>GARD HYPHYMP tests/hbltests/libv3/GARD.wbf<span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="701" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
701
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<td class="new_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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC706" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>FADE HYPHYMP tests/hbltests/libv3/FADE.wbf<span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="702" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="707" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
707
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>NAME GARD </span>
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<td class="new_line diff-line-num new" data-linenumber="708" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
708
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"> COMMAND HYPHYMP </span>
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<td class="new_line diff-line-num new" data-linenumber="709" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
709
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"> tests/hbltests/libv3/GARD.wbf </span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"> <span class="si" style="color: #dd1144;">${</span><span class="nv" style="color: #008080;">HYPHY_ENV_ARG</span><span class="si" style="color: #dd1144;">}</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"> <span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="702" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
702
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>ABSREL HYPHYMP tests/hbltests/libv3/ABSREL.wbf<span class="p">)</span></span>
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<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
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"><span class="c1" style="color: #999988; font-style: italic;">#add_test (FMM HYPHYMP tests/hbltests/libv3/FMM.wbf)</span></span>
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<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
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cmake"><span class="c1" style="color: #999988; font-style: italic;">#add_test (NAME ABSREL-MH COMMAND HYPHYMP tests/hbltests/libv3/ABSREL-MH.wbf)</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#6651ddff6eb82c840ced7c1dddee15c6e1913dd4"><strong style="font-weight: 600;">Dockerfile</strong></a>
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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1" class="line" lang="docker"><span class="k" style="font-weight: 600;">FROM</span><span class="s" style="color: #dd1144;"> ubuntu:24.04</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2" class="line" lang="docker"></span>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="docker"><span class="c" style="color: #999988; font-style: italic;"># Install build dependencies</span></span>
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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
4
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get update <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #dd1144;">\</span></span>
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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="docker"> apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> <span class="nt" style="color: #000080;">-y</span> build-essential cmake</span>
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6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="docker"></span>
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="docker"><span class="c" style="color: #999988; font-style: italic;"># Add a non-root user</span></span>
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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
8
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="docker"><span class="k" style="font-weight: 600;">RUN </span>groupadd <span class="nt" style="color: #000080;">-r</span> hyphyuser <span class="o" style="font-weight: 600;">&&</span> useradd <span class="nt" style="color: #000080;">-r</span> <span class="nt" style="color: #000080;">-g</span> hyphyuser hyphyuser</span>
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9
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10
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="docker"><span class="c" style="color: #999988; font-style: italic;"># Create a directory for the project</span></span>
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<td class="new_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">
11
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="docker"><span class="k" style="font-weight: 600;">WORKDIR</span><span class="s" style="color: #dd1144;"> /hyphy</span></span>
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12
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13
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="docker"><span class="c" style="color: #999988; font-style: italic;"># Copy project files</span></span>
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14
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14" class="line" lang="docker"><span class="k" style="font-weight: 600;">COPY</span><span class="s" style="color: #dd1144;"> ./cmake /hyphy/cmake</span></span>
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15
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC15" class="line" lang="docker"><span class="k" style="font-weight: 600;">COPY</span><span class="s" style="color: #dd1144;"> ./src /hyphy/src</span></span>
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16
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC16" class="line" lang="docker"><span class="k" style="font-weight: 600;">COPY</span><span class="s" style="color: #dd1144;"> ./contrib /hyphy/contrib</span></span>
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17
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC17" class="line" lang="docker"><span class="k" style="font-weight: 600;">COPY</span><span class="s" style="color: #dd1144;"> ./res /hyphy/res</span></span>
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18
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC18" class="line" lang="docker"><span class="k" style="font-weight: 600;">COPY</span><span class="s" style="color: #dd1144;"> CMakeLists.txt /hyphy</span></span>
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19
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC19" class="line" lang="docker"><span class="k" style="font-weight: 600;">COPY</span><span class="s" style="color: #dd1144;"> ./tests /hyphy/tests</span></span>
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20
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC20" class="line" lang="docker"></span>
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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
21
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC21" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span><span class="nb" style="color: #0086b3;">chown</span> <span class="nt" style="color: #000080;">-R</span> hyphyuser:hyphyuser .</span>
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22
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC22" class="line" lang="docker"></span>
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23
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23" class="line" lang="docker"><span class="c" style="color: #999988; font-style: italic;"># Install project</span></span>
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<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
24
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC24" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>cmake <span class="nb" style="color: #0086b3;">.</span> <span class="o" style="font-weight: 600;">&&</span> make <span class="nt" style="color: #000080;">-j</span> <span class="nb" style="color: #0086b3;">install</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC26" class="line" lang="docker"><span class="k" style="font-weight: 600;">USER</span><span class="s" style="color: #dd1144;"> hyphyuser</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong style="font-weight: 600;">README.md</strong></a>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -9,6 +9,20 @@ HyPhy is an open-source software package for the analysis of genetic sequences u</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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10
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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 -c bioconda hyphy`</span></span>
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11
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11
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<td class="old_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
12
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;">#### Running with Docker</span></span>
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<td class="old_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
13
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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">You can also run HyPhy without having to install it on your system using the provided Dockerfile. Following the below instructions starts an interactive Docker container where HyPhy is already available. </span>
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<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
14
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
15
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC15" class="line" lang="markdown">If you don't have Docker installed, first look at <span class="p">[</span><span class="nv" style="color: #008080;">Docker Desktop</span><span class="p">](</span><span class="sx" style="color: #dd1144;">https://docs.docker.com/desktop/</span><span class="p">)</span>.</span>
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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
16
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC16" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
17
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC17" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Please note you must change this code snippet to point to the appropriate location for your input data. This will be made available inside the container at `/hyphy/data`.**</span></span>
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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
18
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC18" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
19
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC19" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="old_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
20
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC20" class="line" lang="markdown">git clone https://github.com/veg/hyphy.git</span>
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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
21
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC21" class="line" lang="markdown">cd hyphy</span>
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<td class="old_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
22
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC22" class="line" lang="markdown">docker build -t hyphy:latest .</span>
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<td class="old_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
23
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23" class="line" lang="markdown">docker run --rm -v [path-to-your-input-data]:/hyphy/data -it hyphy:latest</span>
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<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
24
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC24" class="line" lang="markdown"><span class="p">```</span></span>
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25
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC25" class="line" lang="markdown"></span>
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<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
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<td class="new_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
26
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC26" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Run with Command Line Arguments</span></span>
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<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
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<td class="new_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
27
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC27" class="line" lang="markdown"><span class="sb" style="color: #dd1144;">`hyphy <method_name> --alignment <path_to_alignment_file> <additional_method_specific_arguments>`</span> </span>
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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14
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<td class="new_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
28
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC28" class="line" lang="markdown"><span class="p">+</span> _<span class="sb" style="color: #dd1144;">`<method_name>`</span> is the name of the analysis you wish to run (can be: absrel, bgm, busted, fade, fel, fubar, gard, meme, relax or slac)_</span>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -86,6 +100,27 @@ And then run make install to install the software</td>
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86
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100
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="markdown"><span class="p">+</span> libhyphy_mp.(so/dylib/dll) will be installed at <span class="sb" style="color: #dd1144;">`/location/of/choice/lib`</span></span>
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87
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101
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="markdown"><span class="p">+</span> HyPhy's standard library of batchfiles will go into <span class="sb" style="color: #dd1144;">`/location/of/choice/lib/hyphy`</span></span>
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102
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="markdown"></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Building HyPhy for Web Assembly</span></span>
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104
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="105" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
105
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="markdown">Use <span class="p">[</span><span class="nv" style="color: #008080;">Emscripten</span><span class="p">](</span><span class="sx" style="color: #dd1144;">https://emscripten.org/docs/compiling/Building-Projects.html</span><span class="p">)</span> to produce web assembly files, which can be run entirely within a modern browser. See https://observablehq.com/@spond/hyphy-biowasm for an example. </span>
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106
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
107
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC107" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="old_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="108" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
108
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC108" class="line" lang="markdown">emcmake cmake -DCMAKE_EXE_LINKER_FLAGS="-sTOTAL_STACK=2097152 -02 -sASSERTIONS=1 -sMODULARIZE=1 -sALLOW_MEMORY_GROWTH -sFORCE_FILESYSTEM=1 -sEXIT_RUNTIME=0 -s EXPORTED_RUNTIME_METHODS=["callMain","FS","PROXYFS","WORKERFS","UTF8ToString","getValue","AsciiToString"] -lworkerfs.js -lproxyfs.js -s INVOKE_RUN=0 -s ENVIRONMENT="web,worker" ${EM_FLAGS//-s /-s} -fwasm-exceptions --preload-file res@/hyphy --preload-file tests/hbltests@/tests"</span>
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109
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC109" class="line" lang="markdown"><span class="p">```</span> </span>
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110
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC110" class="line" lang="markdown"></span>
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111
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC111" class="line" lang="markdown"><span class="p">```</span></span>
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112
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC112" class="line" lang="markdown">emmake make -j hyphy </span>
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113
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC113" class="line" lang="markdown"><span class="p">```</span></span>
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114
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115
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC115" class="line" lang="markdown">This creates </span>
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116
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117
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC117" class="line" lang="markdown"><span class="p">```</span></span>
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118
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122
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123
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125
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126
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong style="font-weight: 600;">debian/changelog</strong></a>
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1
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1" class="line" lang="plaintext">hyphy (2.5.68+dfsg-1) unstable; urgency=medium</span>
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2
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3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="plaintext"> * New upstream version 2.5.68+dfsg</span>
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4
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4" class="line" lang="plaintext"> * d/patches/*: unfuzz all patches.</span>
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5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext"> -- Étienne Mollier <emollier@debian.org> Sat, 15 Feb 2025 19:20:03 +0100</span>
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7
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext"></span>
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1
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext">hyphy (2.5.63+dfsg-1) unstable; urgency=medium</span>
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2
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9
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext"></span>
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3
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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext"> * New upstream version 2.5.63+dfsg</span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#63c3307a25f0c1334b59e145f9fc809c05bbfa70"><strong style="font-weight: 600;">debian/patches/rm_arch_specific_flags.patch</strong></a>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -7,7 +7,7 @@ Last-Update: 2020-09-28</td>
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7
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>
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<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
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="diff"><span class="gd" style="color: #000000; background-color: #ffdddd;">--- hyphy.orig/CMakeLists.txt</span></span>
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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
9
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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
9
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="diff"><span class="gi" style="color: #000000; background-color: #ddffdd;">+++ hyphy/CMakeLists.txt</span></span>
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10
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="diff"><span class="p">@@ -19<span class="idiff left deletion" style="background-color: #fac5cd;">5</span>,10 +19<span class="idiff right deletion" style="background-color: #fac5cd;">5</span>,10 @@</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="diff"><span class="p">@@ -19<span class="idiff left addition" style="background-color: #c7f0d2;">8</span>,10 +19<span class="idiff right addition" style="background-color: #c7f0d2;">8</span>,10 @@</span></span>
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<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
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="diff"> #set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -fopt-info")</span>
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12
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12
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="diff"> </span>
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13
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13
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="diff"> if(NOAVX)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" style="width: 35px; 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="20" style="width: 35px; 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">@@ -20,7 +20,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</td>
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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
20
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20
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC20" class="line" lang="diff"> endif()</span>
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21
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21
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC21" class="line" lang="diff"> else(NOSSE4)</span>
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<td class="old_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
22
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<td class="new_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
22
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC22" class="line" lang="diff"> PCL_CHECK_FOR_SSE4()</span>
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<td class="old_line diff-line-num old" data-linenumber="23" 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">
23
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<td class="new_line diff-line-num old" data-linenumber="23" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC23" class="line" lang="diff"><span class="p">@@ -21<span class="idiff left deletion" style="background-color: #fac5cd;">3</span>,7 +21<span class="idiff right deletion" style="background-color: #fac5cd;">3</span>,7 @@</span></span>
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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
23
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23" class="line" lang="diff"><span class="p">@@ -21<span class="idiff left addition" style="background-color: #c7f0d2;">6</span>,7 +21<span class="idiff right addition" style="background-color: #c7f0d2;">6</span>,7 @@</span></span>
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24
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<td class="new_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
24
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC24" class="line" lang="diff"> else(NOAVX)</span>
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<td class="old_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
25
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25
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC25" class="line" lang="diff"> PCL_CHECK_FOR_AVX()</span>
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26
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26
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC26" class="line" lang="diff"> if(${HAVE_AVX_EXTENSIONS})</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="29" style="width: 35px; 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="29" style="width: 35px; 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">@@ -29,7 +29,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</td>
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<td class="old_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
29
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29
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC29" class="line" lang="diff"> add_definitions (-D_SLKP_USE_AVX_INTRINSICS)</span>
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<td class="old_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
30
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<td class="new_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
30
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC30" class="line" lang="diff"> PCL_CHECK_FOR_FMA3()</span>
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<td class="old_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
31
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31
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC31" class="line" lang="diff"> if (${HAVE_FMA3})</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC32" class="line" lang="diff"><span class="p">@@ -2<span class="idiff left deletion" style="background-color: #fac5cd;">48</span>,7 +2<span class="idiff right deletion" style="background-color: #fac5cd;">48</span>,7 @@</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC32" class="line" lang="diff"><span class="p">@@ -2<span class="idiff left addition" style="background-color: #c7f0d2;">51</span>,7 +2<span class="idiff right addition" style="background-color: #c7f0d2;">51</span>,7 @@</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC33" class="line" lang="diff"> if(NOAVX)</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC34" class="line" lang="diff"> if(NOSSE4)</span>
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35
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC35" class="line" lang="diff"> if(NOT CMAKE_SYSTEM_NAME STREQUAL "Emscripten")</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="38" style="width: 35px; 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="38" style="width: 35px; 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">@@ -38,7 +38,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</td>
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<td class="old_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
38
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC38" class="line" lang="diff"> endif()</span>
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39
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39
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC39" class="line" lang="diff"> else(NOSSE4)</span>
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40
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40
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC40" class="line" lang="diff"> PCL_CHECK_FOR_SSE4()</span>
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41
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC41" class="line" lang="diff"><span class="p">@@ -26<span class="idiff left deletion" style="background-color: #fac5cd;">3</span>,7 +26<span class="idiff right deletion" style="background-color: #fac5cd;">3</span>,7 @@</span></span>
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41
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC41" class="line" lang="diff"><span class="p">@@ -26<span class="idiff left addition" style="background-color: #c7f0d2;">6</span>,7 +26<span class="idiff right addition" style="background-color: #c7f0d2;">6</span>,7 @@</span></span>
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42
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42
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC42" class="line" lang="diff"> else(NOAVX)</span>
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43
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43
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC43" class="line" lang="diff"> PCL_CHECK_FOR_AVX()</span>
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44
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC44" class="line" lang="diff"> if(${HAVE_AVX_EXTENSIONS})</span>
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<li id="fae4045e7c53be7e233f4d504a872eab7bffa150">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#fae4045e7c53be7e233f4d504a872eab7bffa150"><strong style="font-weight: 600;">debian/patches/set-zlib-after-setting-default-libs.patch</strong></a>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -5,7 +5,7 @@ Forwarded: not-needed</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5" class="line" lang="diff"><span class="p">Last-Update: 2021-08-25</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="diff"><span class="gd" style="color: #000000; background-color: #ffdddd;">--- hyphy.orig/CMakeLists.txt</span></span>
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7
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="diff"><span class="gi" style="color: #000000; background-color: #ddffdd;">+++ hyphy/CMakeLists.txt</span></span>
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8
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<td class="new_line diff-line-num old" data-linenumber="8" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="diff"><span class="p">@@ -3<span class="idiff left deletion" style="background-color: #fac5cd;">59</span>,15 +3<span class="idiff right deletion" style="background-color: #fac5cd;">59</span>,6 @@</span></span>
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8
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="diff"><span class="p">@@ -3<span class="idiff left addition" style="background-color: #c7f0d2;">62</span>,15 +3<span class="idiff right addition" style="background-color: #c7f0d2;">62</span>,6 @@</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="diff"> add_definitions (-D__HYPHYCURL__)</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="diff"> endif(${CURL_FOUND})</span>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -20,8 +20,8 @@ Last-Update: 2021-08-25</td>
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<td class="new_line diff-line-num old" data-linenumber="23" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC23" class="line" lang="diff"> <span class="idiff left right deletion" style="background-color: #fac5cd;">#-------------------------------------------------------------------------------</span></span>
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<td class="new_line diff-line-num old" data-linenumber="23" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC24" class="line" lang="diff"><span class="p">@@ -42<span class="idiff left deletion" style="background-color: #fac5cd;">2</span>,6 +41<span class="idiff right deletion" style="background-color: #fac5cd;">3</span>,16 @@</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23" class="line" lang="diff"> </span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC24" class="line" lang="diff"><span class="p">@@ -42<span class="idiff left addition" style="background-color: #c7f0d2;">6</span>,6 +41<span class="idiff right addition" style="background-color: #c7f0d2;">7</span>,16 @@</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC25" class="line" lang="diff"> set(SQLITE3_INCLUDE_DIRS ${SQLITE3_INCLUDE_DIR})</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC26" class="line" lang="diff"> endif()</span>
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<li id="d185b62d54557160e7ddc743405a9cec66dcaa96">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#d185b62d54557160e7ddc743405a9cec66dcaa96"><strong style="font-weight: 600;">debian/patches/use_debian_sqlite.patch</strong></a>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -8,7 +8,7 @@ Forwarded: not-needed</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="diff"><span class="gd" style="color: #000000; background-color: #ffdddd;">--- hyphy.orig/CMakeLists.txt</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="diff"><span class="gi" style="color: #000000; background-color: #ddffdd;">+++ hyphy/CMakeLists.txt</span></span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="diff"><span class="p">@@ -15<span class="idiff left deletion" style="background-color: #fac5cd;">5</span>,12 +15<span class="idiff right deletion" style="background-color: #fac5cd;">5</span>,11 @@</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="diff"><span class="p">@@ -15<span class="idiff left addition" style="background-color: #c7f0d2;">6</span>,12 +15<span class="idiff right addition" style="background-color: #c7f0d2;">6</span>,11 @@</span></span>
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12
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="diff"> file(GLOB SRC_CONTRIB src/contrib/*.cpp)</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14" class="line" lang="diff"> set(SRC_LINK src/lib/link/THyPhy.cpp)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" style="width: 35px; 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="22" style="width: 35px; 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">@@ -22,7 +22,7 @@ Forwarded: not-needed</td>
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22
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22
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC22" class="line" lang="diff"> set_source_files_properties(${SRC_CORE} ${SRC_NEW} {SRC_UTILS} PROPERTIES COMPILE_FLAGS "-Weffc++ -Wextra -Wall")</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC23" class="line" lang="diff"> </span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC25" class="line" lang="diff"><span class="p">@@ -39<span class="idiff left deletion" style="background-color: #fac5cd;">3</span>,6 +39<span class="idiff right deletion" style="background-color: #fac5cd;">2</span>,35 @@</span></span>
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25
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC25" class="line" lang="diff"><span class="p">@@ -39<span class="idiff left addition" style="background-color: #c7f0d2;">7</span>,6 +39<span class="idiff right addition" style="background-color: #c7f0d2;">6</span>,35 @@</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC27" class="line" lang="diff"> endif(NOT NODE)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" style="width: 35px; 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="58" style="width: 35px; 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">@@ -58,7 +58,7 @@ Forwarded: not-needed</td>
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58
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58
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59
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59
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC59" class="line" lang="diff"> #-------------------------------------------------------------------------------</span>
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60
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC60" class="line" lang="diff"> # setup some source properties so that we don't spam stdout</span>
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61
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC61" class="line" lang="diff"><span class="p">@@ -40<span class="idiff left deletion" style="background-color: #fac5cd;">3</span>,11 +43<span class="idiff right deletion" style="background-color: #fac5cd;">1</span>,6 @@</span></span>
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61
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC61" class="line" lang="diff"><span class="p">@@ -40<span class="idiff left addition" style="background-color: #c7f0d2;">7</span>,11 +43<span class="idiff right addition" style="background-color: #c7f0d2;">5</span>,6 @@</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="diff"> set_property(</span>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -70,7 +70,7 @@ Forwarded: not-needed</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC70" class="line" lang="diff"> SOURCE src/core/calcnode2.cpp</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC71" class="line" lang="diff"> APPEND_STRING PROPERTY COMPILE_FLAGS " -fstrict-aliasing -funroll-loops"</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC72" class="line" lang="diff"> )</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC73" class="line" lang="diff"><span class="p">@@ -4<span class="idiff left deletion" style="background-color: #fac5cd;">27</span>,7 +45<span class="idiff right deletion" style="background-color: #fac5cd;">0</span>,6 @@</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC73" class="line" lang="diff"><span class="p">@@ -4<span class="idiff left addition" style="background-color: #c7f0d2;">31</span>,7 +45<span class="idiff right addition" style="background-color: #c7f0d2;">4</span>,6 @@</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="diff"> src/core/include</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="diff"> src/contrib</span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#d76a9b9f3a5b58b8ab344a6fc421ce8a9b1af242"><strong style="font-weight: 600;">res/TemplateBatchFiles/F_ST.bf</strong></a>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -242,42 +242,32 @@ if (distanceChoice == "Full likelihood") {</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC243" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (j = 0; j</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;">=i; j = j</span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">1)</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC244" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {</span></span>
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<td class="new_line diff-line-num old" data-linenumber="245" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC245" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (dataType)</span></span>
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<td class="new_line diff-line-num old" data-linenumber="245" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC246" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="245" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
245
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC245" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (dataType == "Codon") {</span></span>
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<td class="new_line diff-line-num" data-linenumber="246" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
246
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC246" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> DataSetFilter twoSpecFilter = CreateFilter (filteredData</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">3</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;">(speciesIndex==i</span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">1)||(speciesIndex==j)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">GeneticCodeExclusions);</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC247" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num old" data-linenumber="248" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC249" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> else</span></span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC250" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
248
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC248" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> else {</span></span>
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251
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<td class="new_line diff-line-num" data-linenumber="249" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
249
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC249" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> DataSetFilter twoSpecFilter = CreateFilter (filteredData</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;">""</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">(speciesIndex==i</span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">1)||(speciesIndex==j));</span></span>
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252
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<td class="new_line diff-line-num" data-linenumber="250" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
250
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC250" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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253
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<td class="new_line diff-line-num old" data-linenumber="251" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC253" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (FREQUENCY_SENSITIVE)</span></span>
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254
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<td class="new_line diff-line-num old" data-linenumber="251" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC254" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {</span></span>
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255
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<td class="new_line diff-line-num old" data-linenumber="251" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC255" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (USE_POSITION_SPECIFIC_FREQS)</span></span>
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256
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<td class="new_line diff-line-num old" data-linenumber="251" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC256" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="251" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
251
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC251" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (FREQUENCY_SENSITIVE) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="252" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
252
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC252" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (USE_POSITION_SPECIFIC_FREQS) {</span></span>
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<td class="old_line diff-line-num" data-linenumber="257" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
257
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<td class="new_line diff-line-num" data-linenumber="253" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
253
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC253" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> HarvestFrequencies (vectorOfFrequencies</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">filteredData</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">3</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;">1);</span></span>
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258
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<td class="new_line diff-line-num" data-linenumber="254" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
254
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC254" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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259
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<td class="new_line diff-line-num old" data-linenumber="255" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC259" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> else</span></span>
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260
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC260" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="255" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
255
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC255" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> else {</span></span>
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<td class="old_line diff-line-num" data-linenumber="261" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
261
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<td class="new_line diff-line-num" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
256
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC256" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> HarvestFrequencies (vectorOfFrequencies</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">twoSpecFilter</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;">1</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">0);</span></span>
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262
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<td class="new_line diff-line-num" data-linenumber="257" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
257
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC257" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="old_line diff-line-num" data-linenumber="263" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
263
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<td class="new_line diff-line-num" data-linenumber="258" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
258
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC258" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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264
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<td class="new_line diff-line-num old" data-linenumber="259" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC264" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (FREQUENCY_SENSITIVE)</span></span>
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265
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<td class="new_line diff-line-num old" data-linenumber="259" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC265" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="266" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="259" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
259
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC259" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (FREQUENCY_SENSITIVE) {</span></span>
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<td class="old_line diff-line-num" data-linenumber="266" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
266
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<td class="new_line diff-line-num" data-linenumber="260" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
260
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC260" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> MULTIPLY_BY_FREQS = PopulateModelMatrix ("modelMatrix"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">vectorOfFrequencies);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="267" 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">
267
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<td class="new_line diff-line-num old" data-linenumber="261" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC267" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (dataType)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="268" 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">
268
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<td class="new_line diff-line-num old" data-linenumber="261" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC268" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="269" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="261" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
261
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC261" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (dataType == "Codon") {</span></span>
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<td class="old_line diff-line-num" data-linenumber="269" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
269
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<td class="new_line diff-line-num" data-linenumber="262" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
262
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC262" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codonFrequencies = BuildCodonFrequencies (vectorOfFrequencies);</span></span>
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<td class="old_line diff-line-num" data-linenumber="270" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
270
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<td class="new_line diff-line-num" data-linenumber="263" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
263
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC263" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> Model pairModel = (modelMatrix</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> codonFrequencies</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> MULTIPLY_BY_FREQS);</span></span>
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<td class="old_line diff-line-num" data-linenumber="271" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
271
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<td class="new_line diff-line-num" data-linenumber="264" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
264
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC264" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="old_line diff-line-num old" data-linenumber="272" 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">
272
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<td class="new_line diff-line-num old" data-linenumber="265" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC272" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> else</span></span>
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273
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<td class="new_line diff-line-num old" data-linenumber="265" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC273" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="274" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="265" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
265
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC265" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> else {</span></span>
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<td class="old_line diff-line-num" data-linenumber="274" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
274
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<td class="new_line diff-line-num" data-linenumber="266" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
266
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC266" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> Model pairModel = (modelMatrix</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> vectorOfFrequencies</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> MULTIPLY_BY_FREQS);</span></span>
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<td class="old_line diff-line-num" data-linenumber="275" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
275
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<td class="new_line diff-line-num" data-linenumber="267" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
267
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC267" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="old_line diff-line-num" data-linenumber="276" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
276
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<td class="new_line diff-line-num" data-linenumber="268" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
268
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC268" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="old_line diff-line-num old" data-linenumber="277" 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">
277
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<td class="new_line diff-line-num old" data-linenumber="269" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC277" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> else</span></span>
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278
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<td class="new_line diff-line-num old" data-linenumber="269" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC278" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {</span></span>
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<td class="old_line diff-line-num old" data-linenumber="279" 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">
279
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<td class="new_line diff-line-num old" data-linenumber="269" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC279" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (i</span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">j==0)</span></span>
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280
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC280" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {</span></span>
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269
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC269" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> else {</span></span>
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270
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC270" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (i</span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">j==0) {</span></span>
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281
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<td class="new_line diff-line-num" data-linenumber="271" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
271
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC271" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> MULTIPLY_BY_FREQS = PopulateModelMatrix ("modelMatrix"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">equalFreqs);</span></span>
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282
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<td class="new_line diff-line-num" data-linenumber="272" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
272
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC272" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> Model pairModel = (modelMatrix</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> equalFreqs</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> MULTIPLY_BY_FREQS);</span></span>
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283
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273
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC273" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#817efc81f1180519a6136b50a447433f20cf679d"><strong style="font-weight: 600;">res/TemplateBatchFiles/SelectionAnalyses/FEL.bf</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="610" style="width: 35px; 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="610" style="width: 35px; 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">@@ -610,7 +610,6 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod</td>
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<td class="old_line diff-line-num" data-linenumber="610" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
610
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610
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC610" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> GetString (lfInfo</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> ^lf</span><span class="nf" style="color: #990000; font-weight: 600;">,-</span><span class="c1" style="color: #999988; font-style: italic;">1);</span></span>
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611
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<td class="new_line diff-line-num" data-linenumber="611" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
611
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC611" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> ExecuteCommands (filter_data); </span></span>
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612
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<td class="new_line diff-line-num" data-linenumber="612" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
612
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC612" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> __make_filter ((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>
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613
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<td class="new_line diff-line-num old" data-linenumber="613" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC613" class="line" lang="brainfuck"></span>
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<td class="old_line diff-line-num" data-linenumber="614" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
614
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<td class="new_line diff-line-num" data-linenumber="613" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
613
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC613" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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615
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<td class="new_line diff-line-num" data-linenumber="614" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
614
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC614" 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;">SetEnvVariable ("USE_LAST_RESULTS"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> TRUE);</span></span>
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615
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC615" class="line" lang="brainfuck"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="724" style="width: 35px; 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="723" style="width: 35px; 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">@@ -724,9 +723,6 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod</td>
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724
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723
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC723" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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725
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724
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC724" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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726
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725
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC725" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num old" data-linenumber="726" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC727" 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);</span></span>
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728
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<td class="new_line diff-line-num old" data-linenumber="726" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC728" 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 (lfe);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="729" 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">
729
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<td class="new_line diff-line-num old" data-linenumber="726" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC729" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> //assert (0);</span></span>
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<td class="old_line diff-line-num" data-linenumber="730" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
730
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<td class="new_line diff-line-num" data-linenumber="726" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
726
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC726" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="old_line diff-line-num" data-linenumber="731" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
731
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<td class="new_line diff-line-num" data-linenumber="727" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
727
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC727" 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</span></span>
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<td class="old_line diff-line-num" data-linenumber="732" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
732
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<td class="new_line diff-line-num" data-linenumber="728" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
728
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC728" 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 class="c1" style="color: #999988; font-style: italic;"> {</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="737" style="width: 35px; 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="733" style="width: 35px; 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">@@ -737,6 +733,7 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod</td>
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737
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<td class="new_line diff-line-num" data-linenumber="733" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
733
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC733" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> );</span></span>
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738
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<td class="new_line diff-line-num" data-linenumber="734" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
734
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC734" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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739
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<td class="new_line diff-line-num" data-linenumber="735" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
735
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC735" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="736" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
736
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC736" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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740
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<td class="new_line diff-line-num" data-linenumber="737" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
737
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC737" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (^"fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ci") {</span></span>
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<td class="old_line diff-line-num" data-linenumber="741" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
741
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<td class="new_line diff-line-num" data-linenumber="738" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
738
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC738" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (!sim_mode) {</span></span>
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742
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<td class="new_line diff-line-num" data-linenumber="739" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
739
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC739" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (^"fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">srv") {</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="776" style="width: 35px; 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="773" style="width: 35px; 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">@@ -776,10 +773,13 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod</td>
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<td class="old_line diff-line-num" data-linenumber="776" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
776
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773
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC773" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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777
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774
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC774" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="old_line diff-line-num" data-linenumber="778" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
778
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<td class="new_line diff-line-num" data-linenumber="775" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
775
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC775" class="line" lang="brainfuck"></span>
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<td class="old_line diff-line-num old" data-linenumber="779" 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">
779
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<td class="new_line diff-line-num old" data-linenumber="776" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC779" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> ^"fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha_scaler" = (^"fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha_scaler" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> 3*^"fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">beta_scaler_test")/4;</span></span>
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776
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC776" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> ^"fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha_scaler" = <span class="idiff left addition" style="background-color: #c7f0d2;">(Min </span>(^"fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha_scaler"</span><span class="nf" style="color: #990000; font-weight: 600;"><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;"> 100)</span> </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> 3*<span class="idiff addition" style="background-color: #c7f0d2;">Min(</span>^"fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">beta_scaler_test"</span><span class="nf" style="color: #990000; font-weight: 600;"><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;">100)</span>)/4;</span></span>
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777
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC777" class="line" lang="brainfuck"><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;">SetConstraint ("fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">beta_scaler_test"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">"fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha_scaler"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "");</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC778" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC782" 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);</span></span>
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779
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC779" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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780
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC780" 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</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> {</span></span>
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781
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC781" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "OPTIMIZATION_METHOD" : "coordinate</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">wise" </span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC782" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> });</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> if (sim_mode) {</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#bc98d7300147ce39ef8ee0f9b35f3252bebd01d2"><strong style="font-weight: 600;">res/TemplateBatchFiles/SelectionAnalyses/MEME.bf</strong></a>
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<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">@@ -284,7 +284,7 @@ if (meme.run_full_mg94) {</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><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;">run_options</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">retain_lf_object: TRUE</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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285
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285
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><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;">run_options</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">apply_user_constraints: meme</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">define_constraints</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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286
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><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;">run_options</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">optimization_settings: {</span></span>
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287
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "OPTIMIZATION_METHOD" : "coordinate</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">wise"</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff left right addition" style="background-color: #c7f0d2;">//</span>"OPTIMIZATION_METHOD" : "coordinate</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">wise"</span></span>
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288
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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289
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289
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><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;"> meme</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">partitioned_mg_results);</span></span>
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290
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="946" style="width: 35px; 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="946" style="width: 35px; 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">@@ -946,6 +946,7 @@ lfunction meme.apply_initial_estimates (spec) {</td>
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946
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<td class="new_line diff-line-num" data-linenumber="946" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
946
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC946" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (t</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">d;in;spec) {</span></span>
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947
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<td class="new_line diff-line-num" data-linenumber="947" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
947
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC947" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (None != d</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"init"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">) {</span></span>
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948
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<td class="new_line diff-line-num" data-linenumber="948" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
948
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC948" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (Type (d</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;">) == "String") {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="949" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
949
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC949" 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 (d</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 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;"> d</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"init"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">);</span></span>
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949
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<td class="new_line diff-line-num" data-linenumber="950" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
950
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC950" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> ^(d</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;">) = d</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"init"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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951
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC951" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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951
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952
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC952" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="983" style="width: 35px; 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="984" style="width: 35px; 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">@@ -983,6 +984,7 @@ lfunction meme.handle_a_site (lf_fel, lf_bsrel, filter_data, partition_index, pa</td>
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983
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<td class="new_line diff-line-num" data-linenumber="984" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
984
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC984" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha = (((scaler_mapping</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;">synonymous_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>
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984
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<td class="new_line diff-line-num" data-linenumber="985" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
985
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC985" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">beta_fg = (((scaler_mapping</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">'FEL</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">FG'</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;">nonsynonymous_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>
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<td class="old_line diff-line-num" data-linenumber="985" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
985
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<td class="new_line diff-line-num" data-linenumber="986" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
986
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC986" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">beta_bg = (((scaler_mapping</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;">nonsynonymous_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>
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987
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC987" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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986
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988
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC988" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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987
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989
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC989" 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;">apply_initial_estimates (scaler_mapping</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>
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988
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990
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC990" 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;">apply_initial_estimates (scaler_mapping</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"FEL</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">FG"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1002" style="width: 35px; 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="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">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1002,20 +1004,22 @@ lfunction meme.handle_a_site (lf_fel, lf_bsrel, filter_data, partition_index, pa</td>
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1002
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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<td class="old_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
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> bsrel_tree_id = (lfInfo</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"Trees"</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>
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1004
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<td class="new_line diff-line-num" data-linenumber="1006" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1006
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1006" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="old_line diff-line-num new" data-linenumber="1005" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1007" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1007
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1007" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> init_alpha = ^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1008" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1008
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1008" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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1005
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<td class="new_line diff-line-num" data-linenumber="1009" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1009
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1009" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> character_map = None; </span></span>
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1006
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<td class="new_line diff-line-num" data-linenumber="1010" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1010
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1010" class="line" lang="brainfuck"></span>
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<td class="old_line diff-line-num" data-linenumber="1007" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1007
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<td class="new_line diff-line-num" data-linenumber="1011" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1011
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1011" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (rate_count == 2) {</span></span>
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<td class="old_line diff-line-num" data-linenumber="1008" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1008
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<td class="new_line diff-line-num" data-linenumber="1012" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1012
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1012" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> // separate clauses for initial parameter values</span></span>
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<td class="old_line diff-line-num" data-linenumber="1009" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1009
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<td class="new_line diff-line-num" data-linenumber="1013" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1013
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1013" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if ( ^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> ^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">beta_fg) { // FEL estimated beta </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> alpha</span></span>
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1010
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<td class="new_line diff-line-num old" data-linenumber="1014" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1010" 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;">set_ith_omega (scaler_mapping</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;"> 0</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;"><span class="idiff left right deletion" style="background-color: #fac5cd;">25</span></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;">25);</span></span>
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1014
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1014" 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;">set_ith_omega (scaler_mapping</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;"> 0</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;"><span class="idiff left right addition" style="background-color: #c7f0d2;">0</span></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;">25);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1011" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1011
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<td class="new_line diff-line-num" data-linenumber="1015" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1015
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1015" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else { // FEL estimated beta </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;">= alpha</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1012" 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">
1012
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<td class="new_line diff-line-num old" data-linenumber="1016" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1012" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff left right deletion" style="background-color: #fac5cd;">0</span>) {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1013" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1016" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1016
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1016" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff left addition" style="background-color: #c7f0d2;">1e</span></span><span class="nf" style="color: #990000; font-weight: 600;"><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;">5</span>) {</span></span>
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<td class="old_line diff-line-num" data-linenumber="1013" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1013
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<td class="new_line diff-line-num" data-linenumber="1017" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1017
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1017" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> omega_rate = ^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">beta_fg / ^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1014" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1014
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<td class="new_line diff-line-num" data-linenumber="1018" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1018
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1018" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="old_line diff-line-num" data-linenumber="1015" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1015
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<td class="new_line diff-line-num" data-linenumber="1019" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1019
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1019" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> omega_rate = 1;</span></span>
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1016
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<td class="new_line diff-line-num" data-linenumber="1020" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1020
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1020" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="old_line diff-line-num" data-linenumber="1017" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1017
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<td class="new_line diff-line-num" data-linenumber="1021" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1021
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1021" 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;">set_ith_omega (scaler_mapping</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;"> omega_rate</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;">75);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1018" 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">
1018
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<td class="new_line diff-line-num old" data-linenumber="1022" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1018" 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;">set_ith_omega (scaler_mapping</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;"> 1</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">5*^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha </span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> None);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1022" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1022
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1022" 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;">set_ith_omega (scaler_mapping</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;"> <span class="idiff left addition" style="background-color: #c7f0d2;">Max (0</span></span><span class="nf" style="color: #990000; font-weight: 600;"><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;">1</span></span><span class="nf" style="color: #990000; font-weight: 600;"><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;"> </span>1</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">5*^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha<span class="idiff right addition" style="background-color: #c7f0d2;">)</span> </span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> None);</span></span>
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1019
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<td class="new_line diff-line-num" data-linenumber="1023" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1023
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1023" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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1020
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<td class="new_line diff-line-num" data-linenumber="1024" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1024
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1024" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="old_line diff-line-num" data-linenumber="1021" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1021
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<td class="new_line diff-line-num" data-linenumber="1025" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1025
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1025" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> rate</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;">mixture_weight1 = ((scaler_mapping</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"OMEGA"</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;">weights"</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>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1092,14 +1096,14 @@ lfunction meme.handle_a_site (lf_fel, lf_bsrel, filter_data, partition_index, pa</td>
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<td class="old_line diff-line-num" data-linenumber="1092" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1092
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<td class="new_line diff-line-num" data-linenumber="1096" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1096
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1096" 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;">set_ith_omega (scaler_mapping</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;"> 0</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">5</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;">5);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1093" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1093
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<td class="new_line diff-line-num" data-linenumber="1097" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1097
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1097" 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;">set_ith_omega (scaler_mapping</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 2</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;">5</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> None);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1094" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1094
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<td class="new_line diff-line-num" data-linenumber="1098" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1098
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1098" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else { // FEL estimated beta </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;">= alpha</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1095" 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">
1095
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<td class="new_line diff-line-num old" data-linenumber="1099" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1095" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff left right deletion" style="background-color: #fac5cd;">0</span>) {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1096" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1099" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1099
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1099" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff left addition" style="background-color: #c7f0d2;">1e</span></span><span class="nf" style="color: #990000; font-weight: 600;"><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;">5</span>) {</span></span>
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<td class="old_line diff-line-num" data-linenumber="1096" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1096
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<td class="new_line diff-line-num" data-linenumber="1100" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1100
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1100" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> omega_rate = ^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">beta_fg / ^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha;</span></span>
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1097
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<td class="new_line diff-line-num" data-linenumber="1101" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1101
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1101" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="old_line diff-line-num" data-linenumber="1098" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1098
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<td class="new_line diff-line-num" data-linenumber="1102" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1102
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1102" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> omega_rate = 1;</span></span>
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1099
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<td class="new_line diff-line-num" data-linenumber="1103" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1103
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1103" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="old_line diff-line-num" data-linenumber="1100" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1100
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<td class="new_line diff-line-num" data-linenumber="1104" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1104
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1104" 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;">set_ith_omega (scaler_mapping</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;"> omega_rate</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;">5);</span></span>
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1101
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<td class="new_line diff-line-num" data-linenumber="1105" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1105
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1105" 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;">set_ith_omega (scaler_mapping</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;"> Min (1</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> Max (0</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">5</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">omega_rate*2))</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;">5);</span></span>
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1102
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<td class="new_line diff-line-num old" data-linenumber="1106" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1102" 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;">set_ith_omega (scaler_mapping</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 2</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;">5*^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha </span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> None);</span></span>
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1106
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1106" 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;">set_ith_omega (scaler_mapping</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff left addition" style="background-color: #c7f0d2;">Max (0</span></span><span class="nf" style="color: #990000; font-weight: 600;"><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;">1</span></span><span class="nf" style="color: #990000; font-weight: 600;"><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;"> </span>1</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">5*^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha<span class="idiff right addition" style="background-color: #c7f0d2;">)</span> </span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> None);</span></span>
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1103
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1107
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1107" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="old_line diff-line-num" data-linenumber="1104" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1104
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<td class="new_line diff-line-num" data-linenumber="1108" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1108
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1108" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="old_line diff-line-num" data-linenumber="1105" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1105
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<td class="new_line diff-line-num" data-linenumber="1109" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1109
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1109" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> rate</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;">mixture_weight1 = ((scaler_mapping</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"OMEGA"</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;">weights"</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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1191" style="width: 35px; 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="1195" style="width: 35px; 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">@@ -1191,7 +1195,7 @@ lfunction meme.handle_a_site (lf_fel, lf_bsrel, filter_data, partition_index, pa</td>
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<td class="old_line diff-line-num" data-linenumber="1191" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1191
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<td class="new_line diff-line-num" data-linenumber="1195" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1195
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1195" 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;">set_ith_omega (scaler_mapping</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 2</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;">5</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;">5);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1192" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1192
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<td class="new_line diff-line-num" data-linenumber="1196" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1196
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1196" 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;">set_ith_omega (scaler_mapping</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 3</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> ^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">beta_fg</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> None);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1193" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1193
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<td class="new_line diff-line-num" data-linenumber="1197" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1197
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1197" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else { // FEL estimated beta </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;">= alpha</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1194" 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">
1194
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<td class="new_line diff-line-num old" data-linenumber="1198" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1194" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff left right deletion" style="background-color: #fac5cd;">0</span>) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1198" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1198
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1198" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff left addition" style="background-color: #c7f0d2;">1e</span></span><span class="nf" style="color: #990000; font-weight: 600;"><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;">5</span>) {</span></span>
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1195
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<td class="new_line diff-line-num" data-linenumber="1199" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1199
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1199" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> omega_rate = ^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">beta_fg / ^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha;</span></span>
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1196
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<td class="new_line diff-line-num" data-linenumber="1200" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1200
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1200" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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1197
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<td class="new_line diff-line-num" data-linenumber="1201" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1201
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1201" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> omega_rate = 1;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1199" style="width: 35px; 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="1203" style="width: 35px; 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">@@ -1199,7 +1203,7 @@ lfunction meme.handle_a_site (lf_fel, lf_bsrel, filter_data, partition_index, pa</td>
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1199
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1203
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1203" 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;">set_ith_omega (scaler_mapping</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;"> omega_rate</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;">5);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1200" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1200
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<td class="new_line diff-line-num" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1204
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1204" 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;">set_ith_omega (scaler_mapping</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;"> Min (1</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> omega_rate*0</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">25)</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;">5);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1201" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1201
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<td class="new_line diff-line-num" data-linenumber="1205" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1205
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1205" 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;">set_ith_omega (scaler_mapping</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> Min (1</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;">5*omega_rate) </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;">5);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1202" 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">
1202
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<td class="new_line diff-line-num old" data-linenumber="1206" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1202" 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;">set_ith_omega (scaler_mapping</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 3</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;">5*^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha </span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> None);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1206" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1206
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1206" 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;">set_ith_omega (scaler_mapping</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 3</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff left addition" style="background-color: #c7f0d2;">Max (0</span></span><span class="nf" style="color: #990000; font-weight: 600;"><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;">1</span></span><span class="nf" style="color: #990000; font-weight: 600;"><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;"> </span>1</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">5*^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha<span class="idiff right addition" style="background-color: #c7f0d2;">)</span> </span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> None);</span></span>
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1203
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<td class="new_line diff-line-num" data-linenumber="1207" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1207
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1207" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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1204
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<td class="new_line diff-line-num" data-linenumber="1208" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1208
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1208" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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1205
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<td class="new_line diff-line-num" data-linenumber="1209" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1209
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1209" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> rate</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;">mixture_weight1 = ((scaler_mapping</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"OMEGA"</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;">weights"</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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1309" style="width: 35px; 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="1313" style="width: 35px; 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">@@ -1309,7 +1313,8 @@ lfunction meme.handle_a_site (lf_fel, lf_bsrel, filter_data, partition_index, pa</td>
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1309
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<td class="new_line diff-line-num" data-linenumber="1313" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1313
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1313" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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1310
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<td class="new_line diff-line-num" data-linenumber="1314" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1314
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1314" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="old_line diff-line-num" data-linenumber="1311" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1311
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<td class="new_line diff-line-num" data-linenumber="1315" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1315
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1315" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="old_line diff-line-num old" data-linenumber="1312" 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">
1312
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<td class="new_line diff-line-num old" data-linenumber="1316" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1312" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> ^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha = ^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha; </span></span>
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<td class="new_line diff-line-num new" data-linenumber="1316" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1316
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1316" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> ^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha = Min (100</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha); </span></span>
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<td class="new_line diff-line-num new" data-linenumber="1317" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1317
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1317" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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1313
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<td class="new_line diff-line-num" data-linenumber="1318" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1318
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1318" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> // SLKP 20201028 : without this</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> there are occasional initialization issues with </span></span>
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1314
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<td class="new_line diff-line-num" data-linenumber="1319" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1319
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1319" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> // the likelihood function below</span></span>
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1315
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1320
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1320" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1317" style="width: 35px; 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="1322" style="width: 35px; 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">@@ -1317,9 +1322,10 @@ lfunction meme.handle_a_site (lf_fel, lf_bsrel, filter_data, partition_index, pa</td>
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1317
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<td class="new_line diff-line-num" data-linenumber="1322" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1322
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1322" 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_bsrel</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> {</span></span>
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<td class="old_line diff-line-num" data-linenumber="1318" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1318
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<td class="new_line diff-line-num" data-linenumber="1323" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1323
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1323" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "OPTIMIZATION_METHOD" : "nedler</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">mead"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="1319" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1319
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<td class="new_line diff-line-num" data-linenumber="1324" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1324
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1324" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "OPTIMIZATION_START_GRID" : initial_guess_grid</span></span>
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1320
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<td class="new_line diff-line-num old" data-linenumber="1325" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1320" 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;">5</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1325" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1325
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1325" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> //</span><span class="nf" style="color: #990000; font-weight: 600;"><span class="idiff left right addition" style="background-color: #c7f0d2;">,</span></span><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;">5</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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1321
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<td class="new_line diff-line-num" data-linenumber="1326" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1326
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1326" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> });</span></span>
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1322
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<td class="new_line diff-line-num" data-linenumber="1327" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1327
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1327" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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1328
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1328" class="line" lang="brainfuck"></span>
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1323
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<td class="new_line diff-line-num" data-linenumber="1329" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1329
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1329" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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1324
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<td class="new_line diff-line-num" data-linenumber="1330" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1330
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1330" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> /*after_opt = {</span></span>
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1325
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<td class="new_line diff-line-num" data-linenumber="1331" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1331
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1331" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "alpha" : Eval("meme</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">site_alpha")</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1337" style="width: 35px; 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="1343" style="width: 35px; 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">@@ -1337,7 +1343,14 @@ lfunction meme.handle_a_site (lf_fel, lf_bsrel, filter_data, partition_index, pa</td>
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1337
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<td class="new_line diff-line-num" data-linenumber="1343" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1343
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1343" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> alternative = estimators</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ExtractMLEsOptions (lf_bsrel</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> model_mapping</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;">globals_only" : TRUE});</span></span>
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1338
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1344
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1344" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> alternative </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;">fit</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">log_likelihood")</span><span class="p">]</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>
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1339
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<td class="new_line diff-line-num" data-linenumber="1345" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1345
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1345" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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1340
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<td class="new_line diff-line-num old" data-linenumber="1346" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1340" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="1346" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1346
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1346" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> /*</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1341" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1347" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1347
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1347" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha / init_alpha </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> 5) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1348" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1348
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1348" 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;"> ^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha / init_alpha);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1349" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1349
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1349" 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 (fel</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"global"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1350" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1350
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1350" 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 (alternative</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"global"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1351" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1351
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1351" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> assert (0);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1352" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1352
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1352" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1353" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1353
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1353" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> */</span></span>
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1341
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<td class="new_line diff-line-num" data-linenumber="1354" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1354
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1354" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> /*</span></span>
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<td class="old_line diff-line-num" data-linenumber="1342" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1342
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<td class="new_line diff-line-num" data-linenumber="1355" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1355
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1355" 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_bsrel);</span></span>
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1343
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<td class="new_line diff-line-num" data-linenumber="1356" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1356
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1356" 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 (lfe);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1422" style="width: 35px; 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="1435" style="width: 35px; 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">@@ -1422,7 +1435,7 @@ lfunction meme.handle_a_site (lf_fel, lf_bsrel, filter_data, partition_index, pa</td>
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<td class="old_line diff-line-num" data-linenumber="1422" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1422
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<td class="new_line diff-line-num" data-linenumber="1435" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1435
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1435" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="old_line diff-line-num" data-linenumber="1423" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1423
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<td class="new_line diff-line-num" data-linenumber="1436" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1436
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1436" class="line" lang="brainfuck"></span>
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<td class="old_line diff-line-num" data-linenumber="1424" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1424
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1437
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1437" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> ^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">beta_fg := ^rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fel</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">alpha;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1425" 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">
1425
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<td class="new_line diff-line-num old" data-linenumber="1438" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1425" 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_bsrel</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> {"OPTIMIZATION_METHOD" : "<span class="idiff left deletion" style="background-color: #fac5cd;">nedler</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 right deletion" style="background-color: #fac5cd;">mead</span>"});</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1426" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1438" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1438
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1438" 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_bsrel</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> {"OPTIMIZATION_METHOD" : "<span class="idiff left addition" style="background-color: #c7f0d2;">coordinate</span></span><span class="nf" style="color: #990000; font-weight: 600;"><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;">wise</span>"});</span></span>
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1426
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<td class="new_line diff-line-num" data-linenumber="1439" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1439
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1439" class="line" lang="brainfuck"></span>
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<td class="old_line diff-line-num" data-linenumber="1427" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1427
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<td class="new_line diff-line-num" data-linenumber="1440" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1440
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1440" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (sim_mode) {</span></span>
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<td class="old_line diff-line-num" data-linenumber="1428" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1428
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<td class="new_line diff-line-num" data-linenumber="1441" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1441
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1441" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return lrt </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> 2*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>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#cf5243a3058ebeab74574f8cd2c771cd63a43208"><strong style="font-weight: 600;">res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="276" style="width: 35px; 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="276" style="width: 35px; 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">@@ -276,7 +276,7 @@ relax.do_srv = io.SelectAnOption (</td>
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<td class="old_line diff-line-num" data-linenumber="276" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
276
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<td class="new_line diff-line-num" data-linenumber="276" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
276
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC276" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">if (relax</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">do_srv == "Branch</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">site") {</span></span>
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<td class="old_line diff-line-num" data-linenumber="277" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
277
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<td class="new_line diff-line-num" data-linenumber="277" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
277
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC277" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> relax</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">do_bs_srv = TRUE;</span></span>
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<td class="old_line diff-line-num" data-linenumber="278" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
278
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<td class="new_line diff-line-num" data-linenumber="278" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
278
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC278" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> relax</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">do_srv = TRUE;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="279" 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">
279
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<td class="new_line diff-line-num old" data-linenumber="279" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC279" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff left deletion" style="background-color: #fac5cd;">(relax</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;">json</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;">terms</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;">json</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;">analysis</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;">)</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;">terms</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;">settings</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 right deletion" style="background-color: #fac5cd;"> =</span> "Branch</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">site synonymous rate variation";</span></span>
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<td class="old_line diff-line-num new" data-linenumber="280" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="279" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
279
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC279" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff left addition" style="background-color: #c7f0d2;">selection</span></span><span class="nf" style="color: #990000; font-weight: 600;"><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;">io</span></span><span class="nf" style="color: #990000; font-weight: 600;"><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;">json_store_setting (relax</span></span><span class="nf" style="color: #990000; font-weight: 600;"><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;">json</span></span><span class="nf" style="color: #990000; font-weight: 600;"><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;"> "SRV type"</span></span><span class="nf" style="color: #990000; font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="c1" style="color: #999988; font-style: italic;"> "Branch</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">site synonymous rate variation"<span class="idiff right addition" style="background-color: #c7f0d2;">)</span>;</span></span>
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<td class="old_line diff-line-num" data-linenumber="280" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
280
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<td class="new_line diff-line-num" data-linenumber="280" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
280
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC280" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">} else {</span></span>
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<td class="old_line diff-line-num" data-linenumber="281" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
281
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<td class="new_line diff-line-num" data-linenumber="281" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
281
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC281" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (relax</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">do_srv == "Yes") {</span></span>
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282
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<td class="new_line diff-line-num" data-linenumber="282" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
282
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC282" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> relax</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">do_bs_srv = FALSE;</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#8e3fdf8188fef4d3dee842226d22c54f017ec2a1"><strong style="font-weight: 600;">res/TemplateBatchFiles/SelectionAnalyses/error-filter.bf</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="274" style="width: 35px; 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">@@ -274,10 +274,14 @@ for (s;in;TipName (efilter.T,-1)) {</td>
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<td class="old_line diff-line-num" data-linenumber="274" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
274
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<td class="new_line diff-line-num" data-linenumber="274" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
274
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC274" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> fprintf (efilter</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">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;"> s</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;"> efilter</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">sequences</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">s</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>
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275
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<td class="new_line diff-line-num" data-linenumber="275" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
275
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC275" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="276" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
276
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<td class="new_line diff-line-num" data-linenumber="276" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
276
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC276" class="line" lang="brainfuck"></span>
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<td class="old_line diff-line-num new" data-linenumber="277" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="277" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
277
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC277" 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 ("INCLUDE_MODEL_SPECS"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> TRUE);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="278" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
278
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC278" class="line" lang="brainfuck"></span>
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<td class="old_line diff-line-num" data-linenumber="277" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
277
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<td class="new_line diff-line-num" data-linenumber="279" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
279
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC279" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">if (efilter</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">input</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;">json</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">partition_count</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> == 1) {</span></span>
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278
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<td class="new_line diff-line-num" data-linenumber="280" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
280
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC280" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> fprintf (efilter</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">path</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;"> Format (efilter</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">T</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;">0));</span></span>
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279
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<td class="new_line diff-line-num" data-linenumber="281" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
281
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC281" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
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280
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<td class="new_line diff-line-num" data-linenumber="282" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
282
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC282" class="line" lang="brainfuck"></span>
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<td class="old_line diff-line-num new" data-linenumber="281" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="283" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
283
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC283" 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 ("INCLUDE_MODEL_SPECS"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> None);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="284" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
284
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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<td class="old_line diff-line-num" data-linenumber="281" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
281
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="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;">ReportProgressMessageMD ("efilter"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">"results"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">"\nMasked a total of **`efilter</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">total_filtered`** or `Format (efilter</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">total_filtered/efilter</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">input</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;">json</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">sequences</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">/efilter</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">input</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;">json</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;">*100</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;">3)`% sites");</span></span>
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282
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#c079be28c5231888d711d5c41d1be180223dfce6"><strong style="font-weight: 600;">res/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf</strong></a>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -266,11 +266,13 @@ function load_file (prefix) {</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC266" 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>
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267
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267
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC267" 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>
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268
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268
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC268" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> */</span></span>
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269
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<td class="new_line diff-line-num old" data-linenumber="269" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC269" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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270
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<td class="new_line diff-line-num old" data-linenumber="269" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC270" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (_key_</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> _value_; in; partitions_and_trees) {</span></span>
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<td class="old_line diff-line-num old" data-linenumber="271" 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">
271
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<td class="new_line diff-line-num old" data-linenumber="269" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC271" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> (partitions_and_trees</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">_key_</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;">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;">filter_string")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = </span></span>
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272
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<td class="new_line diff-line-num old" data-linenumber="269" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC272" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> selection</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><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;">adjust_partition_string (_value_</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;">filter_string")</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 3*codon_data_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>
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273
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<td class="new_line diff-line-num old" data-linenumber="269" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC273" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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269
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC269" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="270" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
270
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC270" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="271" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
271
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC271" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (_key_</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> _value_; in; partitions_and_trees) {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="274" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="272" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
272
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC272" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> (partitions_and_trees</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">_key_</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;">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;">filter_string")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = </span></span>
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<td class="new_line diff-line-num new" data-linenumber="273" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
273
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC273" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> selection</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><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;">adjust_partition_string (_value_</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;">filter_string")</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 3*codon_data_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>
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274
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC275" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC276" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } </span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC277" class="line" lang="brainfuck"></span>
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278
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC278" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="453" style="width: 35px; 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="455" style="width: 35px; 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">@@ -453,7 +455,8 @@ function doGTR (prefix) {</td>
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<td class="old_line diff-line-num" data-linenumber="453" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
453
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<td class="new_line diff-line-num" data-linenumber="455" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
455
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC455" class="line" lang="brainfuck"><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;">nucleotideRate ("A"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">"C") : { 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;">fit</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MLE") : 0</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">25} </span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="454" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
454
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<td class="new_line diff-line-num" data-linenumber="456" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
456
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC456" class="line" lang="brainfuck"><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;">nucleotideRate ("A"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">"T") : { 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;">fit</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MLE") : 0</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">25} </span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="455" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
455
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<td class="new_line diff-line-num" data-linenumber="457" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
457
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC457" class="line" lang="brainfuck"><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;">nucleotideRate ("C"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">"G") : { 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;">fit</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MLE") : 0</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">25} </span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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456
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<td class="new_line diff-line-num old" data-linenumber="458" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC456" class="line" lang="brainfuck"><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;">nucleotideRate ("G"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">"T") : { 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;">fit</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MLE") : 0</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">25}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="458" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
458
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC458" class="line" lang="brainfuck"><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;">nucleotideRate ("G"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">"T") : { 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;">fit</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MLE") : 0</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">25} </span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="459" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
459
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC459" class="line" lang="brainfuck"><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;">nucleotideRate ("C"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">"T") : { 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;">fit</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MLE") : 1</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">00}</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC460" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC461" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> });</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC462" class="line" lang="brainfuck"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="528" style="width: 35px; 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">@@ -525,7 +528,12 @@ function doGTR (prefix) {</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC528" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (i = 0; i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> partition_count; i</span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">=1) {</span></span>
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526
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529
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC529" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> (partitions_and_trees</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 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;">data</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">tree"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = trees</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>
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527
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530
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC530" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="531" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
531
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC531" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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528
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<td class="new_line diff-line-num" data-linenumber="532" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
532
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC532" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> store_tree_information ();</span></span>
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533
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC533" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="534" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
534
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC534" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (index</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> tree; in; trees) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="535" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
535
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC535" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> trees</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">AdjustZerosToNearZeros (tree</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> (gtr_results</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;">branch_length"</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;">index</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">);</span></span>
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536
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC536" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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529
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<td class="new_line diff-line-num" data-linenumber="537" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
537
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC537" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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530
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538
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC538" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (kill0 == "Constrain") {</span></span>
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531
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<td class="new_line diff-line-num" data-linenumber="539" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
539
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC539" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> zero_branch_length_constrain = ^"namespace_tag"</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;">constrain_zero_branches";</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#334fd299d2360b619629e049fe5f4caa8e55c130"><strong style="font-weight: 600;">res/TemplateBatchFiles/libv3/models/codon/MG_GTR.bf</strong></a>
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1
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">RequireVersion ("2</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">5</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">60");</span></span>
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2
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2" class="line" lang="brainfuck"></span>
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3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">LoadFunctionLibrary("</span><span class="nf" style="color: #990000; font-weight: 600;">..</span><span class="c1" style="color: #999988; font-style: italic;">/codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">bf");</span></span>
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4
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">LoadFunctionLibrary("</span><span class="nf" style="color: #990000; font-weight: 600;">..</span><span class="c1" style="color: #999988; font-style: italic;">/DNA</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">bf");</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">LoadFunctionLibrary("</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;">bf");</span></span>
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6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">LoadFunctionLibrary("</span><span class="nf" style="color: #990000; font-weight: 600;">..</span><span class="c1" style="color: #999988; font-style: italic;">/frequencies</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">bf");</span></span>
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7
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">LoadFunctionLibrary("</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;">/UtilityFunctions</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">bf");</span></span>
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8
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">LoadFunctionLibrary("MG_REV</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">bf");</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">LoadFunctionLibrary("</span><span class="nf" style="color: #990000; font-weight: 600;">..</span><span class="c1" style="color: #999988; font-style: italic;">/protein</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">bf");</span></span>
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10
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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11
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">/** @module models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">GTR */</span></span>
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12
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">//</span><span class="nf" style="color: #990000; font-weight: 600;">----------------------------------------------------------------------------------------------------------------</span></span>
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14
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
15
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC15" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">lfunction model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MG_GTR</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">prompt_and_define (type</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> code) {</span></span>
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16
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC16" 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 (type);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
17
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC17" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MG_GTR</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ModelDescription(type</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> code);</span></span>
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18
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC18" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC19" class="line" lang="brainfuck"></span>
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20
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC20" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">lfunction models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MG_GTR</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ModelDescription(type</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> code) {</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC22" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
23
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23" 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;">CheckAssertion ("`&type` == '`^'terms</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">global'`'"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "MG_GTR only supports `^'terms</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">global'` type");</span></span>
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<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
24
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC24" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
25
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC25" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> // piggyback on the standard MG_REV model for most of the code</span></span>
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26
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC26" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
27
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC27" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> mg_base = models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MG_REV</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ModelDescription (type</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> code);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
28
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC28" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> mg_base</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;">description")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = "The Muse</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">Gaut 94 codon</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">substitution model coupled with the general time reversible (GTR) model of nucleotide substitution</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> which defines a separate dN/dS ratio for each pair of amino</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">acids";</span></span>
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<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
29
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC29" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> mg_base</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">q_ij")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = "models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MG_GTR</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">_GenerateRate";</span></span>
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<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
30
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC30" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> mg_base</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">post_definition")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = "models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MG_GTR</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">post_definition";</span></span>
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<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
31
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC31" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return mg_base;</span></span>
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32
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC32" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
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33
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC33" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
34
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC34" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">lfunction models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MG_GTR</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">_GenerateRate(fromChar</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> toChar</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> namespace</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> model_type</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> model) {</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC35" class="line" lang="brainfuck"></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC36" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MG_GTR</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">_GenerateRate_generic (fromChar</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> toChar</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> namespace</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> model_type</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
37
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC37" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> model</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;">translation_table")</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
38
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC38" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "alpha"</span><span class="nf" style="color: #990000; font-weight: 600;">,</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;">parameters</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">synonymous_rate")</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
39
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC39" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "omega"</span><span class="nf" style="color: #990000; font-weight: 600;">,</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;">parameters</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">omega_ratio")</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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40
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC40" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> );</span></span>
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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
41
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC41" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
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42
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC42" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
43
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC43" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">/**</span></span>
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<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
44
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC44" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> * @name models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MG_GTR</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">_GenerateRate</span></span>
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45
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC45" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> * @param {Number} fromChar</span></span>
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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
46
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC46" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> * @param {Number} toChar</span></span>
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47
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC47" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> * @param {String} namespace</span></span>
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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
48
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC48" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> * @param {String} model_type</span></span>
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<td class="new_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
49
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC49" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> * @param {Matrix} _tt </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> translation table</span></span>
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50
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC50" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> */</span></span>
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51
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC51" class="line" lang="brainfuck"></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC52" class="line" lang="brainfuck"></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC53" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">lfunction models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MG_GTR</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">_GenerateRate_generic (fromChar</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> toChar</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> namespace</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> model_type</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> _tt</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> alpha</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> alpha_term</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> omega</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> omega_term) {</span></span>
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54
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC54" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
55
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC55" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">p = {};</span></span>
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<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
56
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC56" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">diff = models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">diff</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">complete(fromChar</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> toChar);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="57" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
57
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC57" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> diff_count = utility</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">Array1D (_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">diff);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
58
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC58" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
59
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC59" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (diff_count == 1) {</span></span>
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60
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC60" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
61
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC61" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">p</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">model_type</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = {};</span></span>
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<td class="new_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
62
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC62" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">p</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;">global")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = {};</span></span>
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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
63
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
64
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> nuc_rate = "";</span></span>
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65
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (i = 0; i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> diff_count; i </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
67
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if ((_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">diff</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 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;">diff</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">from")</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;"> (_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">diff</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 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;">diff</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">to")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">) {</span></span>
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<td class="new_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">
68
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> nuc_p = "theta_" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> (_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">diff</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 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;">diff</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">to")</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;"> (_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">diff</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 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;">diff</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">from")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
69
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
70
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC70" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> nuc_p = "theta_" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> (_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">diff</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 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;">diff</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">from")</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;">(_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">diff</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 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;">diff</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">to")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
71
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC71" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
72
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC72" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> nuc_p = parameters</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ApplyNameSpace(nuc_p</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> namespace);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
73
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC73" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> (_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">p</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;">global")</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;">nucleotideRateReversible((_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">diff</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 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;">diff</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">from")</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> (_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">diff</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 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;">diff</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">to")</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;"> = nuc_p;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
74
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
75
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> nuc_rate = parameters</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">AppendMultiplicativeTerm (nuc_rate</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> nuc_p);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
76
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
77
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> rate_entry = nuc_rate;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
79
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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80
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (_tt</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">fromChar</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> != _tt</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">toChar</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
81
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="82" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
82
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC82" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (_tt</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">fromChar</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;"> _tt</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">toChar</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="83" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
83
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC83" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> aa_pair = _tt</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">fromChar</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;"> " and " </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> _tt</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">toChar</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
84
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC84" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> aa_tag = "_" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> _tt</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">fromChar</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;"> _tt</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">toChar</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
85
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC85" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
86
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC86" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> aa_pair = _tt</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">toChar</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;"> " and " </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> _tt</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">fromChar</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
87
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC87" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> aa_tag = "_" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> _tt</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">toChar</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;"> _tt</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">fromChar</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
88
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC88" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
89
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC89" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
90
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC90" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> omega_p = parameters</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ApplyNameSpace (omega </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> aa_tag </span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> namespace);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
91
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC91" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> (_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">p</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">model_type</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;">omega_ratio" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> " for " </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> aa_pair</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = omega_p;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
92
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC92" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
93
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC93" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> rate_entry = parameters</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">AppendMultiplicativeTerm (rate_entry</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> omega_p);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="94" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
94
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> } else {</span></span>
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95
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> _GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">p</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">rate_entry")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = nuc_rate;</span></span>
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96
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> }</span></span>
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97
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<td class="new_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">
98
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> _GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">p</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">rate_entry")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = rate_entry;</span></span>
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99
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
100
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> return _GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">p;</span></span>
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101
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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102
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 class="c1" style="color: #999988; font-style: italic;">lfunction models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MG_GTR</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">post_definition (model) {</span></span>
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104
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<td class="new_line diff-line-num new" data-linenumber="105" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
105
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> for (id; in ; model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">GetParameters_RegExp (model</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;">omega_ratio")) {</span></span>
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106
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 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;">SetValue(id</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;">25);</span></span>
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107
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC107" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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108
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC108" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
109
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC109" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">generic</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">post</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">definition (model);</span></span>
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110
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC110" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
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111
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC111" class="line" lang="brainfuck"></span>
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112
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC112" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">lfunction models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MG_GTR</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">set_branch_length(model</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> value</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> parameter) {</span></span>
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113
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC113" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MG_REV</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">set_branch_length(model</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">value</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">parameter);</span></span>
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114
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC114" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#9f6d2efd39d3afa147f430ca6d771b8d64f20a55"><strong style="font-weight: 600;">res/TemplateBatchFiles/libv3/models/codon/MG_REV_PROPERTIES.bf</strong></a>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -252,7 +252,211 @@ terms.model.MG_REV_PROPERTIES.predefined = {</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC252" class="line" lang="brainfuck"><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;">2306464200526206}</span></span>
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253
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC253" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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254
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC254" 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>
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255
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<td class="new_line diff-line-num old" data-linenumber="255" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC255" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Random" : {</span></span>
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255
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC255" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Random</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2" : {</span></span>
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256
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC256" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Random Factor 1":{</span></span>
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257
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC257" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "A":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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258
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC258" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "C":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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259
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC259" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "D":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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260
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC260" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "E":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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261
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC261" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "F":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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262
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC262" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "G":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="263" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
263
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC263" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "H":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="264" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
264
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC264" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "I":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="265" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
265
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC265" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "K":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="266" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
266
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC266" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "L":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="267" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
267
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC267" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "M":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="268" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
268
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC268" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "N":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="269" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
269
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC269" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "P":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="270" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
270
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC270" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Q":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="271" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
271
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC271" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "R":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="272" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
272
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC272" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "S":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="273" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
273
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC273" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "T":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="274" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
274
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC274" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "V":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="275" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
275
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC275" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "W":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="276" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
276
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC276" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Y":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="277" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
277
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC277" 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>
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<td class="new_line diff-line-num new" data-linenumber="278" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
278
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC278" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Random Factor 2":{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="279" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
279
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC279" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "A":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="280" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
280
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC280" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "C":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="281" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
281
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC281" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "D":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="282" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
282
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC282" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "E":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="283" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
283
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC283" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "F":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="284" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
284
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "G":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="285" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
285
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "H":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="286" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
286
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "I":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "K":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "L":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="289" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
289
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "M":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="290" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
290
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "N":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "P":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Q":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_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">
293
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "R":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="294" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
294
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "S":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="295" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
295
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "T":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="296" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
296
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC296" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "V":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="297" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
297
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "W":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="298" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
298
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Y":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="299" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
299
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Random</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">3" : {</span></span>
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<td class="new_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">
302
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Random Factor 1":{</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "A":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "C":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "D":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "E":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "F":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "G":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "H":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "I":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="311" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
311
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "K":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="312" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
312
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "L":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="313" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
313
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "M":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="314" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
314
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC314" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "N":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="315" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
315
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC315" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "P":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="316" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
316
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC316" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Q":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="317" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
317
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC317" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "R":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="318" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
318
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC318" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "S":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="319" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
319
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC319" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "T":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="320" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
320
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC320" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "V":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="321" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
321
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC321" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "W":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="322" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
322
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC322" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Y":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="323" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
323
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC323" 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>
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<td class="new_line diff-line-num new" data-linenumber="324" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
324
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC324" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Random Factor 2":{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="325" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
325
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC325" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "A":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="326" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
326
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC326" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "C":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="327" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
327
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC327" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "D":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="328" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
328
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC328" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "E":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="329" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
329
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC329" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "F":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="330" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
330
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC330" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "G":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="331" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
331
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC331" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "H":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="332" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
332
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC332" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "I":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="333" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
333
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC333" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "K":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="334" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
334
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC334" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "L":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="335" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
335
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC335" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "M":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="336" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
336
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC336" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "N":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="337" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
337
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC337" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "P":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="338" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
338
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC338" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Q":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
339
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC339" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "R":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="340" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
340
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC340" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "S":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="341" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
341
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC341" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "T":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="342" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
342
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC342" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "V":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="343" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
343
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC343" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "W":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
344
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC344" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Y":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="345" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
345
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC345" 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>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="346" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
346
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC346" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Random Factor 3":{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="347" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
347
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC347" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "A":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="348" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
348
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC348" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "C":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="349" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
349
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC349" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "D":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="350" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
350
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC350" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "E":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="351" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
351
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC351" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "F":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="352" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
352
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC352" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "G":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="353" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
353
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC353" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "H":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="354" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
354
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC354" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "I":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="355" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
355
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC355" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "K":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
356
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC356" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "L":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="357" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
357
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC357" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "M":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="358" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
358
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC358" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "N":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="359" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
359
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC359" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "P":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="360" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
360
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC360" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Q":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="361" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
361
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC361" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "R":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="362" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
362
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC362" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "S":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="363" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
363
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC363" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "T":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="364" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
364
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC364" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "V":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="365" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
365
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC365" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "W":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="366" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
366
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC366" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Y":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="367" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
367
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC367" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
368
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC368" 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>
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<td class="new_line diff-line-num new" data-linenumber="369" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
369
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC369" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Random</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">4" : {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="370" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
370
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC370" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Random Factor 1":{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="371" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
371
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC371" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "A":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="372" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
372
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC372" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "C":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="373" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
373
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC373" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "D":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="374" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
374
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC374" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "E":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="375" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
375
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC375" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "F":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="376" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
376
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC376" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "G":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="377" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
377
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC377" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "H":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="378" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
378
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC378" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "I":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="379" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
379
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC379" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "K":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="380" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
380
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC380" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "L":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="381" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
381
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC381" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "M":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="382" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
382
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC382" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "N":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="383" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
383
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC383" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "P":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="384" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
384
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC384" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Q":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="385" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
385
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC385" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "R":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="386" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
386
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC386" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "S":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="387" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
387
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC387" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "T":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="388" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
388
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC388" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "V":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="389" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
389
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC389" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "W":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="390" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
390
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC390" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Y":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="391" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
391
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC391" 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>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="392" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
392
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC392" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Random Factor 2":{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="393" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
393
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC393" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "A":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="394" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
394
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC394" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "C":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="395" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
395
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC395" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "D":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="396" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
396
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC396" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "E":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="397" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
397
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC397" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "F":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="398" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
398
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC398" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "G":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="399" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
399
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC399" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "H":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
400
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC400" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "I":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="401" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
401
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC401" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "K":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="402" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
402
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC402" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "L":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="403" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
403
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC403" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "M":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="404" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
404
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC404" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "N":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="405" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
405
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC405" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "P":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="406" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
406
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC406" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Q":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="407" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
407
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC407" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "R":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="408" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
408
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC408" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "S":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="409" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
409
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC409" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "T":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
410
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC410" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "V":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="411" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
411
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC411" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "W":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="412" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
412
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC412" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Y":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="413" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
413
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC413" 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>
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<td class="new_line diff-line-num new" data-linenumber="414" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
414
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC414" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Random Factor 3":{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="415" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
415
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC415" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "A":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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416
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC416" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "C":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="417" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
417
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC417" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "D":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="418" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
418
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC418" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "E":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="419" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
419
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC419" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "F":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="420" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
420
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC420" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "G":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="421" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
421
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC421" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "H":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="422" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
422
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC422" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "I":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="423" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
423
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC423" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "K":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="424" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
424
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC424" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "L":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="425" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
425
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC425" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "M":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="426" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
426
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC426" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "N":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="427" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
427
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC427" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "P":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="428" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
428
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC428" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Q":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="429" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
429
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC429" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "R":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="430" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
430
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC430" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "S":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="431" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
431
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC431" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "T":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="432" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
432
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC432" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "V":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="433" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
433
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC433" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "W":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="434" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
434
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC434" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Y":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
435
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC435" 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>
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<td class="new_line diff-line-num new" data-linenumber="436" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
436
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC436" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Random Factor 4":{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="437" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
437
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC437" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "A":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="438" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
438
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC438" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "C":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="439" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
439
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC439" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "D":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="440" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
440
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC440" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "E":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="441" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
441
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC441" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "F":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="442" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
442
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC442" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "G":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="443" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
443
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC443" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "H":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="444" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
444
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC444" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "I":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="445" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
445
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC445" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "K":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="446" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
446
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC446" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "L":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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447
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC447" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "M":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="448" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
448
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC448" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "N":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="449" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
449
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC449" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "P":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="450" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
450
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC450" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Q":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="451" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
451
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC451" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "R":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="452" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
452
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC452" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "S":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="453" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
453
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC453" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "T":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="454" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
454
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC454" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "V":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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455
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC455" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "W":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="456" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
456
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC456" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Y":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span></span>
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457
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC457" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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458
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC458" 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>
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<td class="new_line diff-line-num new" data-linenumber="459" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
459
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC459" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Random</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">5" : {</span></span>
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256
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<td class="new_line diff-line-num" data-linenumber="460" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
460
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC460" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Random Factor 1":{</span></span>
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<td class="old_line diff-line-num" data-linenumber="257" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
257
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<td class="new_line diff-line-num" data-linenumber="461" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
461
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC461" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "A":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="258" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
258
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<td class="new_line diff-line-num" data-linenumber="462" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
462
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC462" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "C":Random(</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -376,7 +580,10 @@ lfunction model.codon.MG_REV_PROPERTIES.prompt_and_define (type, code) {</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {</span></span>
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581
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC581" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Atchley":"Use the five properties derived from a factor analysis of 500 amino</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">acid properties </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">Table 2 in PNAS (2005) 102(18) 6395</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">6400 doi: 10</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">1073/pnas</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">0408677102</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>
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<td class="old_line diff-line-num" data-linenumber="378" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
378
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<td class="new_line diff-line-num" data-linenumber="582" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
582
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC582" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "LCAP":"Use the five properties defined in the Conant and Stadler LCAP model </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">Mol Biol Evol (2009) 26 (5): 1155</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">1161</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;"> doi: 10</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">1093/molbev/msp031</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>
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379
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<td class="new_line diff-line-num old" data-linenumber="583" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC379" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Random" : "Random properties (for null hypothesis testing)"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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583
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC583" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Random</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2" : "Two random properties (for null hypothesis testing)"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="584" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
584
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC584" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Random</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">3" : "Three random properties (for null hypothesis testing)"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="585" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
585
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC585" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Random</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">4" : "Four random properties (for null hypothesis testing)"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="586" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
586
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC586" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Random</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">5" : "Five random properties (for null hypothesis testing)"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num" data-linenumber="587" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC587" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Custom":"Load the set of properties from a file"</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC588" 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 class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="old_line diff-line-num" data-linenumber="382" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC589" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "The set of properties to use in the model");</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="408" style="width: 35px; 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="615" style="width: 35px; 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">@@ -408,6 +615,7 @@ lfunction models.codon.MG_REV_PROPERTIES.ModelDescription(type, code, properties</td>
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<td class="old_line diff-line-num" data-linenumber="408" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
408
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<td class="new_line diff-line-num" data-linenumber="615" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
615
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC615" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> mg_base</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">residue_name_map")</span><span class="p">]</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;">ValidateIDs (utility</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">Keys (mg_base</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">residue_properties")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">));</span></span>
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<td class="new_line diff-line-num" data-linenumber="616" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
616
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC616" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> mg_base</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">post_definition")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = "models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MG_REV_PROPERTIES</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">post_definition";</span></span>
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617
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC617" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> mg_base</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">set_branch_length")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = "models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MG_REV_PROPERTIES</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">set_branch_length";</span></span>
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618
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC618" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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411
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<td class="new_line diff-line-num" data-linenumber="619" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
619
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC619" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return mg_base;</span></span>
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412
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620
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC620" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
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413
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621
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC621" class="line" lang="brainfuck"></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#e8578acaed39aa42e302cfc6b43e09678d292e72"><strong style="font-weight: 600;">res/TemplateBatchFiles/libv3/models/codon/MSS.bf</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; 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="14" style="width: 35px; 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">@@ -14,8 +14,11 @@ terms.model.MSS.syn_rate_within = " within codon class ";</td>
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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14
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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14" class="line" lang="brainfuck"><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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">syn_rate_between = " between codon classes ";</span></span>
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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15
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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15" class="line" lang="brainfuck"><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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">between = "synonymous rate between codon classes";</span></span>
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<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
16
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<td class="new_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
16
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC16" class="line" lang="brainfuck"><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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">neutral = "neutral reference";</span></span>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
17
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC17" class="line" lang="brainfuck"><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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">empirical = "empirical";</span></span>
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17
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<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
18
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC18" class="line" lang="brainfuck"><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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_classes = "codon classes";</span></span>
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<td class="old_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
19
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC19" class="line" lang="brainfuck"><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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_pairs = "codon pairs";</span></span>
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<td class="old_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
18
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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
20
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC20" class="line" lang="brainfuck"><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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">normalize = "normalize rates";</span></span>
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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
21
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC21" class="line" lang="brainfuck"><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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">non_syn_reference = "non</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">synonymous reference";</span></span>
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19
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<td class="new_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
22
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC22" class="line" lang="brainfuck"></span>
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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
23
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC23" 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>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC24" class="line" lang="brainfuck"></span>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -32,7 +35,9 @@ lfunction model.codon.MSS.prompt_and_define_freq (type, code, freq) {</td>
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<td class="old_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
32
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<td class="new_line diff-line-num" data-linenumber="35" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC35" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {"SynREV2g"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "Each pair of synonymous codons mapping to the same amino</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">acid class and separated by a transition have a separate substitution rate (Valine == neutral)</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;"> All between</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">class synonymous substitutions share a rate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">"}</span></span>
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<td class="old_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
33
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<td class="new_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
36
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC36" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {"SynREVCodon"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "Each codon pair that is exchangeable gets its own substitution rate (fully estimated</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> mean = 1)"}</span></span>
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<td class="old_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
34
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<td class="new_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
37
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC37" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {"Random"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "Random partition (specify how many classes; largest class = neutral)"}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
38
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC38" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {"Empirical"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "Load a TSV file with an empirical rate estimate for each codon pair"}</span></span>
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<td class="old_line diff-line-num" data-linenumber="35" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
35
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<td class="new_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
39
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC39" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {"File"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "Load a TSV partition from file (prompted for neutral class)"}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
40
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC40" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {"Codon</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">file"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "Load a TSV partition for pairs of codons from a file (prompted for neutral class)"}</span></span>
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<td class="old_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
36
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<td class="new_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
41
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC41" 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>
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<td class="new_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
42
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC42" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Synonymous Codon Class Definitions");</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC43" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</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">@@ -69,6 +74,17 @@ lfunction model.codon.MSS.prompt_and_define_freq (type, code, freq) {</td>
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69
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74
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="old_line diff-line-num" data-linenumber="71" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
71
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (partitioning_option == "SynREV" || partitioning_option == "SynREVFull" || partitioning_option == "SynREVCodon" ) {</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> KeywordArgument ("mss</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">reference</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">rate"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "Normalize relative to these rates"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "synonymous");</span></span>
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79
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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80
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> reference_option = io</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">SelectAnOption (</span></span>
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<td class="new_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
81
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="82" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
82
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC82" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {"synonymous"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "Synonymous rates have mean 1</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>
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<td class="new_line diff-line-num new" data-linenumber="83" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
83
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC83" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {"non</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">synonymous"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "Non</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">synonymous rates are set to 1</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">"} </span></span>
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<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
84
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC84" 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>
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<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
85
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC85" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "Rate normalization"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
86
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC86" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> );</span></span>
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<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
87
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC87" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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72
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<td class="new_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
88
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC88" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> bins = {};</span></span>
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89
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC89" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> mapping = {};</span></span>
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90
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC90" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> mapping_codon = {};</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="82" style="width: 35px; 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="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">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -82,9 +98,9 @@ lfunction model.codon.MSS.prompt_and_define_freq (type, code, freq) {</td>
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82
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> return models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ModelDescription(type</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> code</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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83
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 class="c1" style="color: #999988; font-style: italic;"> {</span></span>
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<td class="old_line diff-line-num" data-linenumber="84" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
84
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> ^"terms</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_classes" : mapping</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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85
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<td class="new_line diff-line-num old" data-linenumber="101" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC85" class="line" lang="brainfuck"><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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">normalize" : <span class="idiff left right deletion" style="background-color: #fac5cd;">TRUE</span></span></span>
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86
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<td class="new_line diff-line-num old" data-linenumber="101" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC86" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff left deletion" style="background-color: #fac5cd;">//</span>^"terms</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">n<span class="idiff right deletion" style="background-color: #fac5cd;">eutral" : "V</span>"</span></span>
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87
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<td class="new_line diff-line-num old" data-linenumber="101" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC87" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span>}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
101
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> ^"terms</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">normalize" : <span class="idiff left addition" style="background-color: #c7f0d2;">reference_option == "synonymous"</span></span><span class="nf" style="color: #990000; font-weight: 600;"><span class="idiff right addition" style="background-color: #c7f0d2;">,</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
102
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">n<span class="idiff left right addition" style="background-color: #c7f0d2;">on_syn_reference" : reference_option != "synonymous</span>"</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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88
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104
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> );</span></span>
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89
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> }</span></span>
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90
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 class="c1" style="color: #999988; font-style: italic;"> if (partitioning_option == "SynREVFull") {</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="92" style="width: 35px; 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="108" style="width: 35px; 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">@@ -92,8 +108,14 @@ lfunction model.codon.MSS.prompt_and_define_freq (type, code, freq) {</td>
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92
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<td class="new_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
108
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC108" class="line" lang="brainfuck"><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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_classes" : mapping}</span></span>
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93
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109
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC109" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> );</span></span>
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110
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC110" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
111
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC111" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="112" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
112
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC112" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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95
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<td class="new_line diff-line-num" data-linenumber="113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
113
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC113" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ModelDescription(type</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> code</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="96" 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">
96
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<td class="new_line diff-line-num old" data-linenumber="114" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> {^"terms</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_classes" : mapping_codon</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">normalize" : TRUE}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
114
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC114" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
115
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC115" class="line" lang="brainfuck"><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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_classes" : mapping_codon</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="116" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
116
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC116" class="line" lang="brainfuck"><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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">normalize" : reference_option == "synonymous"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="117" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
117
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC117" class="line" lang="brainfuck"><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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">non_syn_reference" : reference_option != "synonymous"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
118
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC118" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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97
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119
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 class="c1" style="color: #999988; font-style: italic;"> );</span></span>
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120
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> }</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> </span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="204" style="width: 35px; 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">@@ -182,6 +204,18 @@ lfunction model.codon.MSS.prompt_and_define_freq (type, code, freq) {</td>
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182
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<td class="new_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
204
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> return models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ModelDescription(type</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> code</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">LoadClasses (null));</span></span>
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183
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<td class="new_line diff-line-num" data-linenumber="205" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
205
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> }</span></span>
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<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
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<td class="new_line diff-line-num" data-linenumber="206" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
206
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> </span></span>
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<td class="old_line diff-line-num new" data-linenumber="185" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 (partitioning_option == "Codon</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">file") {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="185" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> KeywordArgument ("mss</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">file"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "File defining the model partition");</span></span>
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<td class="old_line diff-line-num new" data-linenumber="185" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> KeywordArgument ("mss</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">neutral"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "Designation for the neutral substitution rate");</span></span>
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<td class="old_line diff-line-num new" data-linenumber="185" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> return models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ModelDescription(type</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> code</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">LoadClassesCodon (null));</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> }</span></span>
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212
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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213
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> if (partitioning_option == "Empirical") {</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> KeywordArgument ("mss</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">file"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "File defining empirical rates for each pair of codons");</span></span>
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<td class="new_line diff-line-num new" data-linenumber="215" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
215
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> return models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ModelDescription(type</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> code</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">LoadEmpiricalRates (null));</span></span>
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216
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<td class="new_line diff-line-num new" data-linenumber="217" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
217
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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218
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC218" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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185
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219
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC219" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return {};</span></span>
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220
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC220" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
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221
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC221" class="line" lang="brainfuck"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="209" style="width: 35px; color: rgba(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="243" style="width: 35px; 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">@@ -209,6 +243,10 @@ lfunction models.codon.MSS.ModelDescription(type, code, codon_classes) {</td>
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<td class="old_line diff-line-num" data-linenumber="209" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
209
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<td class="new_line diff-line-num" data-linenumber="243" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
243
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC243" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> m</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">q_ij")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = "models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">_GenerateRate";</span></span>
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<td class="old_line diff-line-num" data-linenumber="210" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
210
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<td class="new_line diff-line-num" data-linenumber="244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
244
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC244" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> m</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_classes")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = codon_classes </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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_classes"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="211" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
211
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<td class="new_line diff-line-num" data-linenumber="245" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
245
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC245" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> m</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">neutral")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = codon_classes </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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">neutral"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="old_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">
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<td class="new_line diff-line-num new" data-linenumber="246" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
246
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC246" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> m</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">empirical")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = codon_classes </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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">empirical"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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247
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC247" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> m</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_pairs")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = codon_classes </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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_pairs"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="old_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">
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<td class="new_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
248
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC248" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> m</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">non_syn_reference")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = codon_classes </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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">non_syn_reference"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="old_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">
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<td class="new_line diff-line-num new" data-linenumber="249" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
249
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC249" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="old_line diff-line-num" data-linenumber="212" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
212
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<td class="new_line diff-line-num" data-linenumber="250" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
250
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC250" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (codon_classes/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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">between")) {</span></span>
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<td class="old_line diff-line-num" data-linenumber="213" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
213
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<td class="new_line diff-line-num" data-linenumber="251" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
251
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC251" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> m</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">between"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = codon_classes </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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">between"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="214" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
214
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<td class="new_line diff-line-num" data-linenumber="252" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
252
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC252" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="225" style="width: 35px; 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="263" style="width: 35px; 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">@@ -225,6 +263,9 @@ lfunction models.codon.MSS.ModelDescription(type, code, codon_classes) {</td>
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<td class="old_line diff-line-num" data-linenumber="225" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
225
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<td class="new_line diff-line-num" data-linenumber="263" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
263
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC263" class="line" lang="brainfuck"></span>
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<td class="old_line diff-line-num" data-linenumber="226" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
226
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<td class="new_line diff-line-num" data-linenumber="264" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
264
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC264" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">lfunction models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">post_definition (model) {</span></span>
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<td class="old_line diff-line-num" data-linenumber="227" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
227
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<td class="new_line diff-line-num" data-linenumber="265" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
265
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC265" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">// TBD</span></span>
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<td class="old_line diff-line-num new" data-linenumber="228" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="266" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
266
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC266" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (model</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">non_syn_reference"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="267" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
267
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC267" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="268" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
268
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC268" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="old_line diff-line-num" data-linenumber="228" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
228
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<td class="new_line diff-line-num" data-linenumber="269" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
269
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC269" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> rates = model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">GetParameters_RegExp (model</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;"> 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;">parameters</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">synonymous_rate"));</span></span>
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<td class="old_line diff-line-num" data-linenumber="229" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
229
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<td class="new_line diff-line-num" data-linenumber="270" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
270
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC270" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> D = utility</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">Array1D (rates);</span></span>
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<td class="old_line diff-line-num" data-linenumber="230" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
230
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<td class="new_line diff-line-num" data-linenumber="271" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
271
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC271" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> w = 1 / D;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="257" style="width: 35px; 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="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">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -257,6 +298,9 @@ lfunction models.codon.MSS._GenerateRate (fromChar, toChar, namespace, model_typ</td>
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<td class="old_line diff-line-num" data-linenumber="257" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
257
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> alpha_term = 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;">parameters</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">synonymous_rate");</span></span>
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<td class="old_line diff-line-num" data-linenumber="258" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
258
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> beta_term = 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;">parameters</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">nonsynonymous_rate");</span></span>
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<td class="old_line diff-line-num" data-linenumber="259" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
259
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<td class="new_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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> nr = model</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">neutral")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="260" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> empirical = model</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">empirical")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="260" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_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">
302
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon_pairs = model</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_pairs")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="260" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> non_syn_ref = model</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">non_syn_reference")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="260" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
260
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<td class="new_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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> omega = "omega";</span></span>
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<td class="old_line diff-line-num" data-linenumber="261" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
261
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<td class="new_line diff-line-num" data-linenumber="305" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
305
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> alpha = "alpha";</span></span>
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<td class="old_line diff-line-num" data-linenumber="262" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
262
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<td class="new_line diff-line-num" data-linenumber="306" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
306
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> beta = "beta";</span></span>
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<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="332" style="width: 35px; 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">@@ -288,73 +332,98 @@ lfunction models.codon.MSS._GenerateRate (fromChar, toChar, namespace, model_typ</td>
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<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
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<td class="new_line diff-line-num" data-linenumber="332" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
332
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC332" class="line" lang="brainfuck"></span>
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<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
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<td class="new_line diff-line-num" data-linenumber="333" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
333
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC333" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (_tt</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">fromChar</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> != _tt</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">toChar</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">) {</span></span>
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290
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<td class="new_line diff-line-num" data-linenumber="334" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
334
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC334" class="line" lang="brainfuck"></span>
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<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
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<td class="new_line diff-line-num old" data-linenumber="335" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (model_type == 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;">global")) {</span></span>
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292
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<td class="new_line diff-line-num old" data-linenumber="335" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> aa_rate = parameters</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ApplyNameSpace(omega</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> namespace);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="293" 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">
293
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<td class="new_line diff-line-num old" data-linenumber="335" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> (_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">p</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">model_type</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;">omega_term</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = aa_rate;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="294" 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">
294
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<td class="new_line diff-line-num old" data-linenumber="335" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="old_line diff-line-num old" data-linenumber="295" 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">
295
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<td class="new_line diff-line-num old" data-linenumber="335" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> aa_rate = beta;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="296" 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">
296
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<td class="new_line diff-line-num old" data-linenumber="335" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC296" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> (_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">p</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">model_type</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;">beta_term</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = aa_rate;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="297" 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">
297
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<td class="new_line diff-line-num old" data-linenumber="335" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="old_line diff-line-num old" data-linenumber="298" 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">
298
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<td class="new_line diff-line-num old" data-linenumber="335" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> rate_entry </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;"> aa_rate;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="299" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="335" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
335
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC335" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (!non_syn_ref) {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="299" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="336" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
336
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC336" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (model_type == 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;">global")) {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="299" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="337" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
337
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC337" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> aa_rate = parameters</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ApplyNameSpace(omega</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> namespace);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="299" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="338" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
338
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC338" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> (_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">p</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">model_type</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;">omega_term</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = aa_rate;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
339
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC339" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="299" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="340" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
340
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC340" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> aa_rate = beta;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="299" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="341" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
341
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC341" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> (_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">p</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">model_type</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;">beta_term</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = aa_rate;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="342" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
342
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC342" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="old_line diff-line-num new" data-linenumber="299" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="343" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
343
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC343" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> rate_entry </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;"> aa_rate;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
344
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC344" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } </span></span>
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<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
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<td class="new_line diff-line-num" data-linenumber="345" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
345
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC345" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<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
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<td class="new_line diff-line-num" data-linenumber="346" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
346
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC346" class="line" lang="brainfuck"></span>
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<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
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<td class="new_line diff-line-num old" data-linenumber="347" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> class_from = (model</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_classes"</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;">fromChar</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="302" 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">
302
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<td class="new_line diff-line-num old" data-linenumber="347" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> class_to = (model</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_classes"</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;">toChar</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="old_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">
303
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<td class="new_line diff-line-num old" data-linenumber="347" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="old_line diff-line-num old" data-linenumber="304" 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">
304
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<td class="new_line diff-line-num old" data-linenumber="347" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="old_line diff-line-num old" data-linenumber="305" 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">
305
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<td class="new_line diff-line-num old" data-linenumber="347" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if ((Abs (class_from) && Abs (class_to)) == FALSE) {</span></span>
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<td class="old_line diff-line-num old" data-linenumber="306" 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">
306
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<td class="new_line diff-line-num old" data-linenumber="347" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> class_from = (model</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_classes"</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;">fromChar</span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">toChar</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="307" 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">
307
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<td class="new_line diff-line-num old" data-linenumber="347" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> class_to = class_from;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="308" 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">
308
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<td class="new_line diff-line-num old" data-linenumber="347" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="old_line diff-line-num old" data-linenumber="309" 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">
309
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<td class="new_line diff-line-num old" data-linenumber="347" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="old_line diff-line-num old" data-linenumber="310" 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">
310
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<td class="new_line diff-line-num old" data-linenumber="347" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> assert (Abs (class_from) && Abs (class_to)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "The neutral class for `fromChar` to `toChar` is not specified in the model definition");</span></span>
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<td class="old_line diff-line-num old" data-linenumber="311" 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">
311
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<td class="new_line diff-line-num old" data-linenumber="347" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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<td class="old_line diff-line-num old" data-linenumber="312" 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">
312
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<td class="new_line diff-line-num old" data-linenumber="347" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (class_from == class_to) {</span></span>
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<td class="old_line diff-line-num old" data-linenumber="313" 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">
313
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<td class="new_line diff-line-num old" data-linenumber="347" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (class_from == nr) {</span></span>
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<td class="old_line diff-line-num old" data-linenumber="314" 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">
314
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<td class="new_line diff-line-num old" data-linenumber="347" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC314" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (model_type == 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;">local")) {</span></span>
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315
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<td class="new_line diff-line-num old" data-linenumber="347" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC315" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon_rate = alpha </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;"> class_from;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="316" 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">
316
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<td class="new_line diff-line-num old" data-linenumber="347" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC316" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> (_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">p</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">model_type</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;">alpha_term </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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">syn_rate_within" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> class_from</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = codon_rate;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="317" 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">
317
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<td class="new_line diff-line-num old" data-linenumber="347" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC317" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> rate_entry </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;"> codon_rate;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="318" 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">
318
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<td class="new_line diff-line-num old" data-linenumber="347" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC318" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="old_line diff-line-num old" data-linenumber="319" 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">
319
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<td class="new_line diff-line-num old" data-linenumber="347" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC319" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> rate_entry = nuc_rate;</span></span>
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320
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<td class="new_line diff-line-num old" data-linenumber="347" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC320" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="347" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
347
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC347" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (empirical) {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="321" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="348" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
348
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC348" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (fromChar </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> toChar) {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="321" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="349" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
349
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC349" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> key = fromChar </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;"> toChar;</span></span>
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<td class="old_line diff-line-num" data-linenumber="321" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
321
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<td class="new_line diff-line-num" data-linenumber="350" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
350
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC350" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="old_line diff-line-num old" data-linenumber="322" 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">
322
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<td class="new_line diff-line-num old" data-linenumber="351" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC322" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (model_type == 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;">local")) {</span></span>
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<td class="old_line diff-line-num old" data-linenumber="323" 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">
323
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<td class="new_line diff-line-num old" data-linenumber="351" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC323" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon_rate = alpha </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;"> class_from;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="351" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
351
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC351" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> key = toChar </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;"> fromChar; </span></span>
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<td class="new_line diff-line-num new" data-linenumber="352" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
352
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC352" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="353" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
353
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC353" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="old_line diff-line-num new" data-linenumber="324" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="354" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
354
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC354" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> assert (model</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_classes"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> / key</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "Rate for codon pair `key` was missing from the empirical file definition");</span></span>
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355
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC355" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> rate_entry </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;"> (model</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_classes"</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;">key</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
356
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC356" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="357" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
357
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC357" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="358" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
358
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC358" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (codon_pairs) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="359" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
359
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC359" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (fromChar </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> toChar) {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="324" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="360" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
360
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC360" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> key = fromChar </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;"> toChar;</span></span>
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324
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<td class="new_line diff-line-num" data-linenumber="361" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
361
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC361" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="old_line diff-line-num old" data-linenumber="325" 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">
325
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<td class="new_line diff-line-num old" data-linenumber="362" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC325" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff left deletion" style="background-color: #fac5cd;">codon_rate = parameters</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;">ApplyNameSpace(alp</span>ha </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> "<span class="idiff deletion" style="background-color: #fac5cd;">_</span>" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff deletion" style="background-color: #fac5cd;">class_from</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 right deletion" style="background-color: #fac5cd;"> namespace);</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="362" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
362
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC362" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff left addition" style="background-color: #c7f0d2;">key = toC</span>ha<span class="idiff addition" style="background-color: #c7f0d2;">r</span> </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> "<span class="idiff addition" style="background-color: #c7f0d2;">|</span>" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff right addition" style="background-color: #c7f0d2;">fromChar; </span></span></span>
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326
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<td class="new_line diff-line-num" data-linenumber="363" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
363
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC363" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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327
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<td class="new_line diff-line-num old" data-linenumber="364" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC327" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> (_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">p</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">model_type</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;">alpha_term </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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">syn_rate_within" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> class_from</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = codon_rate;</span></span>
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328
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<td class="new_line diff-line-num old" data-linenumber="364" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC328" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> rate_entry </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;"> codon_rate;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="329" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="364" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
364
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC364" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> assert (model</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_classes"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> / key</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "Rate for codon pair `key` was missing from the empirical file definition");</span></span>
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<td class="old_line diff-line-num new" data-linenumber="329" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="365" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
365
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC365" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> class_from = (model</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_classes"</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;">key</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="366" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
366
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC366" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> class_to = class_from;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="367" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
367
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC367" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else { </span></span>
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<td class="old_line diff-line-num new" data-linenumber="329" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
368
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC368" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> class_from = (model</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_classes"</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;">fromChar</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="329" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="369" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
369
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC369" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> class_to = (model</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_classes"</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;">toChar</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="329" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
329
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<td class="new_line diff-line-num" data-linenumber="370" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
370
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC370" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="old_line diff-line-num old" data-linenumber="330" 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">
330
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<td class="new_line diff-line-num old" data-linenumber="371" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC330" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="old_line diff-line-num old" data-linenumber="331" 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">
331
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<td class="new_line diff-line-num old" data-linenumber="371" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC331" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (class_from </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> class_to) {</span></span>
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<td class="old_line diff-line-num old" data-linenumber="332" 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">
332
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<td class="new_line diff-line-num old" data-linenumber="371" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC332" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon_rate = class_to;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="371" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
371
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC371" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="372" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
372
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC372" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="373" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
373
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC373" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if ((Abs (class_from) && Abs (class_to)) == FALSE) {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="333" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="374" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
374
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC374" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> class_from = (model</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_classes"</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;">fromChar</span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">toChar</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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333
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<td class="new_line diff-line-num" data-linenumber="375" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
375
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC375" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> class_to = class_from;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="334" 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">
334
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<td class="new_line diff-line-num old" data-linenumber="376" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC334" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> class_from = codon_rate;</span></span>
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335
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<td class="new_line diff-line-num" data-linenumber="376" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
376
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC376" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="old_line diff-line-num old" data-linenumber="336" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
336
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<td class="new_line diff-line-num old" data-linenumber="377" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC336" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (Abs (between_rate)) {</span></span>
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<td class="old_line diff-line-num old" data-linenumber="337" 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">
337
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<td class="new_line diff-line-num old" data-linenumber="377" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC337" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (model_type == 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;">local")) {</span></span>
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338
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<td class="new_line diff-line-num old" data-linenumber="377" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC338" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon_rate = between_rate;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="377" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
377
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC377" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="378" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
378
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC378" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> assert (Abs (class_from) && Abs (class_to)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "The neutral class for `fromChar` to `toChar` is not specified in the model definition");</span></span>
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<td class="new_line diff-line-num new" data-linenumber="379" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
379
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC379" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="380" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
380
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC380" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (class_from == class_to) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="381" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
381
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC381" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (class_from == nr) {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="382" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
382
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC382" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (model_type == 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;">local")) {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="383" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
383
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC383" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon_rate = alpha </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;"> class_from;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="384" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
384
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC384" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> (_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">p</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">model_type</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;">alpha_term </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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">syn_rate_within" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> class_from</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = codon_rate;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="385" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
385
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC385" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> rate_entry </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;"> codon_rate;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="386" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
386
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC386" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="387" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
387
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC387" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> rate_entry = nuc_rate;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="388" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
388
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC388" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="old_line diff-line-num" data-linenumber="339" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
339
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<td class="new_line diff-line-num" data-linenumber="389" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
389
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC389" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="old_line diff-line-num old" data-linenumber="340" 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">
340
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<td class="new_line diff-line-num old" data-linenumber="390" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC340" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon_rate = parameters</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ApplyNameSpace(between_rate</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> namespace);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="341" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="390" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
390
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC390" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (model_type == 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;">local")) {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="341" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="391" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
391
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC391" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon_rate = alpha </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;"> class_from;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="392" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
392
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC392" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="341" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="393" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
393
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC393" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon_rate = parameters</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ApplyNameSpace(alpha </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;"> class_from</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> namespace);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="394" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
394
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC394" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="395" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
395
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC395" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> (_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">p</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">model_type</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;">alpha_term </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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">syn_rate_within" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> class_from</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = codon_rate;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="396" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
396
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC396" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> rate_entry </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;"> codon_rate;</span></span>
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<td class="old_line diff-line-num" data-linenumber="341" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
341
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<td class="new_line diff-line-num" data-linenumber="397" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
397
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC397" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="old_line diff-line-num old" data-linenumber="342" 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">
342
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<td class="new_line diff-line-num old" data-linenumber="398" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC342" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> (_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">p</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">model_type</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">between"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = codon_rate;</span></span>
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343
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<td class="new_line diff-line-num old" data-linenumber="398" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC343" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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344
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<td class="new_line diff-line-num" data-linenumber="398" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
398
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC398" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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345
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<td class="new_line diff-line-num old" data-linenumber="399" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC345" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (class_from </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> class_to == nr) {</span></span>
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346
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<td class="new_line diff-line-num old" data-linenumber="399" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC346" 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 ("NEUTRAL");</span></span>
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<td class="old_line diff-line-num old" data-linenumber="347" 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">
347
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<td class="new_line diff-line-num old" data-linenumber="399" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC347" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon_rate = 1;</span></span>
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348
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<td class="new_line diff-line-num old" data-linenumber="399" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC348" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="399" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
399
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC399" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (class_from </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> class_to) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
400
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC400" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon_rate = class_to;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="401" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
401
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC401" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> class_to = class_from;</span></span>
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402
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC402" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> class_from = codon_rate;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="403" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
403
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC403" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="404" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
404
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC404" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (Abs (between_rate)) {</span></span>
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<td class="old_line diff-line-num" data-linenumber="349" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
349
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<td class="new_line diff-line-num" data-linenumber="405" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
405
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC405" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (model_type == 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;">local")) {</span></span>
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<td class="old_line diff-line-num old" data-linenumber="350" 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">
350
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<td class="new_line diff-line-num old" data-linenumber="406" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC350" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon_rate = <span class="idiff left deletion" style="background-color: #fac5cd;">alpha </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;"> "_" </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;"> class_from </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;"> "_" </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 right deletion" style="background-color: #fac5cd;"> class_to</span>;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="351" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="406" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
406
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC406" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon_rate = <span class="idiff left right addition" style="background-color: #c7f0d2;">between_rate</span>;</span></span>
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<td class="old_line diff-line-num" data-linenumber="351" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
351
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<td class="new_line diff-line-num" data-linenumber="407" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
407
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC407" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="old_line diff-line-num old" data-linenumber="352" 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">
352
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<td class="new_line diff-line-num old" data-linenumber="408" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC352" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon_rate = parameters</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ApplyNameSpace(alpha </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;"> class_from </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;"> class_to</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> namespace);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="408" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
408
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC408" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon_rate = parameters</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ApplyNameSpace(between_rate</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> namespace);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="409" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
409
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC409" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
410
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC410" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> (_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">p</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">model_type</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">between"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = codon_rate;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="411" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
411
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC411" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="412" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
412
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC412" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="413" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
413
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC413" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (class_from </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> class_to == nr) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="414" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
414
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC414" 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 ("NEUTRAL");</span></span>
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<td class="new_line diff-line-num new" data-linenumber="415" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
415
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC415" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon_rate = 1;</span></span>
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416
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC416" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="417" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
417
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC417" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (model_type == 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;">local")) {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="353" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="418" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
418
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC418" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon_rate = alpha </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;"> class_from </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;"> class_to;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="419" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
419
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC419" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="353" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="420" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
420
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC420" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon_rate = parameters</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ApplyNameSpace(alpha </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;"> class_from </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;"> class_to</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> namespace);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="421" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
421
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC421" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="422" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
422
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC422" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> (_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">p</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">model_type</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;">alpha_term </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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">syn_rate_between" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> class_from </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> " and " </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> class_to</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = codon_rate;</span></span>
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353
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<td class="new_line diff-line-num" data-linenumber="423" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
423
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC423" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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354
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<td class="new_line diff-line-num old" data-linenumber="424" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC354" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> (_GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">p</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">model_type</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;">alpha_term </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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">syn_rate_between" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> class_from </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> " and " </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> class_to</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = codon_rate;</span></span>
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355
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<td class="new_line diff-line-num" data-linenumber="424" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
424
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC424" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="425" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
425
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC425" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> rate_entry </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;"> codon_rate;</span></span>
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356
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<td class="new_line diff-line-num" data-linenumber="426" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
426
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC426" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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357
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<td class="new_line diff-line-num old" data-linenumber="427" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC357" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> rate_entry </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;"> codon_rate;</span></span>
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358
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<td class="new_line diff-line-num" data-linenumber="427" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
427
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC427" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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359
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<td class="new_line diff-line-num" data-linenumber="428" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
428
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC428" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -363,6 +432,27 @@ lfunction models.codon.MSS._GenerateRate (fromChar, toChar, namespace, model_typ</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC432" class="line" lang="brainfuck"></span>
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433
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC433" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return _GenerateRate</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">p;</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC434" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC435" class="line" lang="brainfuck"></span>
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436
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC436" 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>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC437" class="line" lang="brainfuck"></span>
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438
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC438" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">lfunction models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">LoadEmpiricalRates (file) {</span></span>
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439
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC439" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="440" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
440
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC440" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> SetDialogPrompt ("A TSV file with three columns (Codon1</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> Codon2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> Empirical Rate) which is used to define relative synonymous substitution rates");</span></span>
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<td class="new_line diff-line-num new" data-linenumber="441" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
441
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC441" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> classes = io</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ReadDelimitedFile (file</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "\t"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> TRUE);</span></span>
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442
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC442" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> headers = utility</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">Array1D(classes</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;">io</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">header'</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="443" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
443
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC443" 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;">CheckAssertion("`&headers`</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;">=3"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "Expected a TSV file with at least 3 columns; 2nd column is the codon</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 3rd is the class for this codon");</span></span>
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444
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC444" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon_pairs = {};</span></span>
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<td class="new_line diff-line-num new" data-linenumber="445" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
445
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC445" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (_record_; in; classes </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;">io</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">rows"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">) {</span></span>
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446
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC446" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (_record_</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;"> _record_</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;">) {</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC447" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> key = _record_</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;"> _record_</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;">;</span></span>
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448
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC448" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="449" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
449
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC449" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> key = _record_</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;"> </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;"> _record_</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>
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450
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC450" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="451" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
451
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC451" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon_pairs </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">key</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = Eval (_record_</span><span class="p">[</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>
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<td class="new_line diff-line-num new" data-linenumber="452" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
452
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC452" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="453" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
453
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC453" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="454" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
454
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC454" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return {^"terms</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_classes" : codon_pairs</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">empirical" : TRUE};</span></span>
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455
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC455" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
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456
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC456" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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457
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC457" 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>
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458
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC458" class="line" lang="brainfuck"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="391" style="width: 35px; 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="481" style="width: 35px; 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">@@ -391,3 +481,37 @@ lfunction models.codon.MSS.LoadClasses (file) {</td>
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391
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<td class="new_line diff-line-num" data-linenumber="481" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
481
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC481" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="old_line diff-line-num" data-linenumber="392" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
392
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<td class="new_line diff-line-num" data-linenumber="482" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
482
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC482" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return {^"terms</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_classes" : codons_by_class</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">neutral" : nr};</span></span>
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393
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483
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC483" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
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484
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC484" class="line" lang="brainfuck"></span>
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485
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC485" 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>
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<td class="new_line diff-line-num new" data-linenumber="486" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
486
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC486" class="line" lang="brainfuck"></span>
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<td class="old_line diff-line-num new" data-linenumber="394" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="487" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
487
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC487" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">lfunction models</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">LoadClassesCodon (file) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="488" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
488
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC488" class="line" lang="brainfuck"></span>
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<td class="old_line diff-line-num new" data-linenumber="394" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="489" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
489
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC489" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> SetDialogPrompt ("A TSV file with three columns (Codon1</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> Codon2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> Class) which is used to partition synonymous substitutions into groups");</span></span>
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<td class="old_line diff-line-num new" data-linenumber="394" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="490" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
490
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC490" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> classes = io</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ReadDelimitedFile (file</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "\t"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> TRUE);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="491" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
491
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC491" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> headers = utility</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">Array1D(classes</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;">io</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">header'</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="492" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
492
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC492" 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;">CheckAssertion("`&headers`</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;">=3"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "Expected a TSV file with at least 3 columns; 2nd column is the codon</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 3rd is the class for this codon");</span></span>
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<td class="old_line diff-line-num new" data-linenumber="394" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="493" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
493
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC493" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon_pairs = {};</span></span>
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<td class="new_line diff-line-num new" data-linenumber="494" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
494
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC494" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (_record_; in; classes </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;">io</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">rows"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="495" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
495
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC495" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (_record_</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;"> _record_</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;">) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="496" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
496
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC496" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> key = _record_</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;"> _record_</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;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
497
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC497" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="498" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
498
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC498" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> key = _record_</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;"> </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;"> _record_</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>
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<td class="new_line diff-line-num new" data-linenumber="499" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
499
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC499" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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500
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC500" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon_pairs </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">key</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = _record_</span><span class="p">[</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>
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<td class="new_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
501
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC501" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="502" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
502
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC502" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="503" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
503
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC503" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> classes = utility</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">UniqueValues(codon_pairs);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="504" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
504
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC504" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> class_count = utility</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">Array1D(classes);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="505" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
505
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC505" 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;">CheckAssertion("`&class_count`</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;">=2"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "Expected at least 2 codon classes");</span></span>
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<td class="new_line diff-line-num new" data-linenumber="506" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
506
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC506" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="507" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
507
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> choices = {class_count</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2};</span></span>
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<td class="new_line diff-line-num new" data-linenumber="508" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
508
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (i = 0; i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> class_count; i </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="509" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
509
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> choices</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;">0</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = classes</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>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> choices</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;">1</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = "Codon class " </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> classes</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>
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<td class="new_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">
511
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="512" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
512
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="513" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
513
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> nr= io</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">SelectAnOption (choices</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "Select the codon class which will serve as the neutral rate reference (relative rate = 1)");</span></span>
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514
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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515
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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516
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return {^"terms</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_classes" : codon_pairs</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">neutral" : nr</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;">model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MSS</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_pairs" : TRUE};</span></span>
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517
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#d3ad56ea8debe5ec6fc29c1fb5a1bb44d800352b"><strong style="font-weight: 600;">res/TemplateBatchFiles/libv3/models/frequencies.bf</strong></a>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -230,9 +230,34 @@ lfunction frequencies._aux.validate (model) {</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC230" class="line" lang="brainfuck"></span>
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231
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC231" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
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232
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232
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC232" class="line" lang="brainfuck"></span>
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<td class="old_line diff-line-num new" data-linenumber="233" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="233" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
233
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC233" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">lfunction frequencies</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">_aux</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">pad_zeros (freqs) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="234" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
234
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC234" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> nr = Rows (freqs);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="235" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
235
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC235" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> nc = Columns (freqs);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="236" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
236
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> F = freqs;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="237" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
237
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="238" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
238
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (c = 0; c </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> nc; c </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1) {</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> s = 0;</span></span>
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<td class="new_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">
240
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (r = 0; r </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> nr; r </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="241" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
241
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (freqs </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">r</span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;">c</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>
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<td class="new_line diff-line-num new" data-linenumber="242" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
242
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><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;">= freqs </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">r</span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;">c</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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243
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC243" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> F</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">r</span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;">c</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = freqs </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">r</span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;">c</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
244
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC244" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="245" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
245
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC245" class="line" lang="brainfuck"><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;">= 1e</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">8;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="246" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
246
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC246" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> F</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">r</span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;">c</span><span class="p">]</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;">8;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="247" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
247
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC247" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
248
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC248" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="249" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
249
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC249" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (s </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> 1) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="250" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
250
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC250" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (r = 0; r </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> nr; r </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="251" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
251
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC251" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> F</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">r</span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;">c</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = F</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">r</span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;">c</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">/s;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="252" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
252
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC252" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="253" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
253
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC253" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="254" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
254
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC254" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="255" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
255
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC255" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
256
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC256" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return F;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="257" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
257
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC257" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="258" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
258
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC258" class="line" lang="brainfuck"></span>
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<td class="old_line diff-line-num" data-linenumber="233" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
233
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<td class="new_line diff-line-num" data-linenumber="259" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
259
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC259" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">lfunction frequencies</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">empirical</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">codon_from_nuc (model</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> nuc_dict) {</span></span>
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234
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<td class="new_line diff-line-num" data-linenumber="260" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
260
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC260" class="line" lang="brainfuck"></span>
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235
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<td class="new_line diff-line-num old" data-linenumber="261" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC235" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<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
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<td class="new_line diff-line-num" data-linenumber="261" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
261
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC261" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> result = {model</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">Dimension (model)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">1};</span></span>
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<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
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<td class="new_line diff-line-num" data-linenumber="262" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
262
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC262" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> corrector = 1;</span></span>
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<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
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<td class="new_line diff-line-num" data-linenumber="263" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
263
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC263" 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;">ForEach (model</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;">stop_codons"</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "codon"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="267" style="width: 35px; 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="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">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -267,6 +292,7 @@ lfunction frequencies.empirical.F3x4(model, namespace, datafilter) {</td>
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<td class="old_line diff-line-num" data-linenumber="267" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
267
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> __f = model </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;">efv_estimate"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="268" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
268
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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269
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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<td class="old_line diff-line-num new" data-linenumber="270" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="295" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
295
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> __f = frequencies</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">_aux</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">pad_zeros (__f );</span></span>
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270
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<td class="new_line diff-line-num" data-linenumber="296" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
296
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC296" class="line" lang="brainfuck"></span>
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<td class="old_line diff-line-num" data-linenumber="271" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
271
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> __alphabet = model</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;">bases"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="272" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
272
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> nuc_dict = {};</span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="329" style="width: 35px; 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">@@ -303,6 +329,8 @@ lfunction frequencies.empirical.F1x4(model, namespace, datafilter) {</td>
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<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
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<td class="new_line diff-line-num" data-linenumber="329" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
329
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC329" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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304
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<td class="new_line diff-line-num" data-linenumber="330" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
330
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC330" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> __f = model </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;">efv_estimate"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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305
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<td class="new_line diff-line-num" data-linenumber="331" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
331
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC331" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="332" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
332
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC332" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="333" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
333
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC333" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> __f = frequencies</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">_aux</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">pad_zeros (__f );</span></span>
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306
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334
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC334" class="line" lang="brainfuck"></span>
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<td class="old_line diff-line-num" data-linenumber="307" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
307
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<td class="new_line diff-line-num" data-linenumber="335" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
335
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC335" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> __alphabet = model</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;">bases"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="308" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
308
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<td class="new_line diff-line-num" data-linenumber="336" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
336
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC336" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> nuc_dict = {};</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="338" style="width: 35px; 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="366" style="width: 35px; 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">@@ -338,6 +366,8 @@ lfunction frequencies.empirical.corrected.CF3x4(model, namespace, datafilter) {</td>
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<td class="old_line diff-line-num" data-linenumber="338" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
338
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<td class="new_line diff-line-num" data-linenumber="366" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
366
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC366" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> __f = model </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;">efv_estimate"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="339" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
339
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<td class="new_line diff-line-num" data-linenumber="367" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
367
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC367" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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340
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<td class="new_line diff-line-num" data-linenumber="368" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
368
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC368" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="old_line diff-line-num new" data-linenumber="341" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="369" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
369
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC369" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> __f = frequencies</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">_aux</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">pad_zeros (__f );</span></span>
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<td class="new_line diff-line-num new" data-linenumber="370" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
370
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC370" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="old_line diff-line-num" data-linenumber="341" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
341
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<td class="new_line diff-line-num" data-linenumber="371" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
371
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC371" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> //TODO</span></span>
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<td class="old_line diff-line-num" data-linenumber="342" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
342
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<td class="new_line diff-line-num" data-linenumber="372" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
372
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC372" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> __alphabet = model</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;">alphabet"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="343" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
343
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<td class="new_line diff-line-num" data-linenumber="373" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
373
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC373" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> __estimates = frequencies</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">_aux</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">CF3x4(__f</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> model</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;">bases"</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> __alphabet</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> model</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;">stop_codons"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="462" style="width: 35px; 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="492" style="width: 35px; 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">@@ -462,6 +492,7 @@ function frequencies._aux.empirical.singlechar(model, namespace, datafilter) {</td>
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462
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<td class="new_line diff-line-num" data-linenumber="492" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
492
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC492" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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463
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<td class="new_line diff-line-num" data-linenumber="493" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
493
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC493" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> __f = model </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;">efv_estimate"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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464
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<td class="new_line diff-line-num" data-linenumber="494" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
494
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC494" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="old_line diff-line-num new" data-linenumber="465" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="495" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
495
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC495" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> __f = frequencies</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">_aux</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">pad_zeros (__f );</span></span>
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465
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496
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC496" class="line" lang="brainfuck"></span>
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497
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC497" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> model</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;">efv_estimate</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = __f;</span></span>
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467
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498
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC498" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return model;</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#801d4bca405dfccac3b1e451b211ca98bd00d599"><strong style="font-weight: 600;">res/TemplateBatchFiles/libv3/models/parameters.bf</strong></a>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -853,18 +853,23 @@ lfunction parameters.helper.tree_lengths_to_initial_values(dict, type) {</td>
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853
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853
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC853" class="line" lang="brainfuck"></span>
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854
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<td class="new_line diff-line-num" data-linenumber="854" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
854
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC854" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (i = 0; i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> components; i </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1) {</span></span>
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855
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<td class="new_line diff-line-num" data-linenumber="855" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
855
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC855" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> this_component = {};</span></span>
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<td class="new_line diff-line-num new" data-linenumber="856" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
856
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC856" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (_branch_name_ </span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> _branch_length_; in; (dict</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 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;">branch_length")</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="857" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
857
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC857" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> this_component </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">_branch_name_</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = { </span></span>
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<td class="new_line diff-line-num new" data-linenumber="858" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
858
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC858" 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;">getGlobalValue('terms</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">fit</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MLE') : </span></span>
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<td class="new_line diff-line-num new" data-linenumber="859" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
859
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC859" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> factor*_branch_length_</span></span>
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<td class="new_line diff-line-num new" data-linenumber="860" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
860
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC860" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> };</span></span>
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<td class="new_line diff-line-num new" data-linenumber="861" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
861
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC861" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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856
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862
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC862" class="line" lang="brainfuck"></span>
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857
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<td class="new_line diff-line-num old" data-linenumber="863" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC857" class="line" lang="brainfuck"></span>
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858
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<td class="new_line diff-line-num old" data-linenumber="863" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC858" 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;">ForEachPair((dict</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 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;">branch_length")</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "_branch_name_"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "_branch_length_"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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859
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<td class="new_line diff-line-num old" data-linenumber="863" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC859" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "</span></span>
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860
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<td class="new_line diff-line-num old" data-linenumber="863" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC860" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> `&this_component`</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">_branch_name_</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;">fit</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MLE') : `&factor`*_branch_length_}</span></span>
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861
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC861" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> ");</span></span>
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862
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<td class="new_line diff-line-num old" data-linenumber="863" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC862" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> result</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;"> = this_component;</span></span>
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863
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC863" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (Abs (this_component)) {</span></span>
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864
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC864" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> result</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;"> = this_component;</span></span>
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865
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC865" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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863
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866
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC866" class="line" lang="brainfuck"></span>
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864
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867
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC867" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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865
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868
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC868" class="line" lang="brainfuck"></span>
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866
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<td class="new_line diff-line-num old" data-linenumber="869" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC866" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return { 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;">branch_length"): result</span></span>
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869
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC869" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return { </span></span>
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<td class="new_line diff-line-num new" data-linenumber="870" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
870
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC870" 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;">getGlobalValue("terms</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">branch_length"): result</span></span>
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867
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<td class="new_line diff-line-num" data-linenumber="871" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
871
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC871" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> };</span></span>
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872
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC872" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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868
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873
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC873" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
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869
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874
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC874" class="line" lang="brainfuck"></span>
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870
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875
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC875" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">/**</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#c7933e171033f4eac9d83419583cca5474f9266c"><strong style="font-weight: 600;">res/TemplateBatchFiles/libv3/tasks/estimators.bf</strong></a>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -48,10 +48,10 @@ lfunction estimators.RestoreLFStateFromSnapshot(lf_id, snapshot) {</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC48" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">lfunction estimators</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ConstrainAndRunLRT (lf_id</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> constraint) {</span></span>
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49
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<td class="new_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
49
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC49" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> savedMLES = estimators</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">TakeLFStateSnapshot (lf_id);</span></span>
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<td class="new_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
50
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC50" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> currentLL = estimators</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">ComputeLF (lf_id);</span></span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC51" class="line" lang="brainfuck"></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC51" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num" data-linenumber="52" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC52" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> df = Call (constraint</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> TRUE);</span></span>
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<td class="new_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
53
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC53" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> Optimize (res</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> ^lf_id);</span></span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC54" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC54" 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>
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<td class="new_line diff-line-num" data-linenumber="55" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
55
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC55" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (df </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;">= 0) {</span></span>
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<td class="new_line diff-line-num" data-linenumber="56" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
56
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC56" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> lrt = math</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">DoLRT (res</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="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">currentLL</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">df);</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC57" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#60b4ddbf1a82aaaa07321568533f1dbe54e992ec"><strong style="font-weight: 600;">res/TemplateBatchFiles/libv3/tasks/mapping.bf</strong></a>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">LoadFunctionLibrary("</span><span class="nf" style="color: #990000; font-weight: 600;">..</span><span class="c1" style="color: #999988; font-style: italic;">/IOFunctions</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">bf");</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">LoadFunctionLibrary("</span><span class="nf" style="color: #990000; font-weight: 600;">..</span><span class="c1" style="color: #999988; font-style: italic;">/all</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;">bf");</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="brainfuck"></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4" class="line" lang="brainfuck"></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">/**</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> * Define scoring parameters for alignment tasks</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> * @name mapping</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">DefineScoringMatrices</span></span>
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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> * @param code </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> genetic code definition</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> * @returns {Dictionary} a structure with various scoring options (opaque)</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> */</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">namespace mapping {</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> lfunction DefineScoringMatrices (code) {</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC15" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC16" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> score_matrix = {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC17" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> { 6</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;">3</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;">4</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;">4</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;">2</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;">2</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;">2</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 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;">3</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;">3</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;">3</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;">2</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;">2</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;">4</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;">2</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;"> </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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">5</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;">3</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 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;">4</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;">2</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;">2</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;">7}</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC18" 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 class="c1" style="color: #999988; font-style: italic;">3</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</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;">4</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;">6</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</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;">5</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;">2</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;">6</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;">4</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">3</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;">5</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;">4</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;">2</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;">3</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;">5</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;">3</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;">5</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;">3</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 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;">2</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;">7}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC19" 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 class="c1" style="color: #999988; font-style: italic;">4</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;">2</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">5</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 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;">2</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;">2</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">6</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;">6</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 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;">4</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;">5</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;">4</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;"> </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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">7</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;">4</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;">5</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 6</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;">2</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;">2</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;">7}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC20" 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 class="c1" style="color: #999988; font-style: italic;">4</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;">4</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;"> 8</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;">6</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;">2</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">3</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;">3</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;">5</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;">6</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;">2</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;">6</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;">6</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;">3</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 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;">3</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;">7</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;">6</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;">6</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 6</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">3</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;">7}</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC21" 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 class="c1" style="color: #999988; font-style: italic;">2</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;">6</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;">5</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;">6</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 10</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;">5</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;">7</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;">5</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;">5</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;">3</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;">3</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;">6</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;">3</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;">5</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;">5</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;">2</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;">2</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;">4</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;">4</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;">2</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;">5</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;">6</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;">4</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;">7}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC22" 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 class="c1" style="color: #999988; font-style: italic;">2</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;"> </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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</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;">5</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;"> 1</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;">4</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">6</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;">4</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;"> </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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">6</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;">3</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 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;">2</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;">3</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;">3</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;">4</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 class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 6</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;">2</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;">7}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23" 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 class="c1" style="color: #999988; font-style: italic;">2</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;">2</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;">2</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">7</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;"> 7</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;">4</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 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;">6</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;">5</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">4</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;">6</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;">3</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 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;">2</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;">5</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;">4</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;">4</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;"> 6</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;">2</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;">7}</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC24" 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 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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">5</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;">2</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;">3</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;">5</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;">4</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;">4</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 7</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;">4</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;">7</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;">6</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;">3</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;">5</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;">5</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;">4</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;">2</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;">4</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;">4</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;">5</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;">6</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;">2</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;">4</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;">4</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;">7}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC25" 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 class="c1" style="color: #999988; font-style: italic;">3</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;">2</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">3</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;">5</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;"> </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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">4</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 10</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;">6</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;">5</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;">2</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;">3</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;">3</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;">4</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;">2</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;">4</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;">5</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">6</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 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 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;">3</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;">7}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC26" 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 class="c1" style="color: #999988; font-style: italic;">3</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;">6</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;">6</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;">5</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;">3</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;">6</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;">6</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;">7</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;">6</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 6</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">5</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;"> </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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">5</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;">5</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;">2</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;">5</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;">3</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 2</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;">5</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;">6</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;">2</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;">7}</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC27" 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 class="c1" style="color: #999988; font-style: italic;">3</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;">4</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;">6</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;">6</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;">3</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;">4</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;">5</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;">6</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;">5</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;"> 6</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;">5</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;"> </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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">5</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;">5</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;">3</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;">3</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;">3</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">6</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;">5</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;">2</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;">7}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC28" 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 class="c1" style="color: #999988; font-style: italic;">2</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;"> </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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</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;">6</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;"> 0</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;">3</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;">2</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;">5</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;">5</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 7</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;">3</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;">6</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;">2</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 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;">2</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;">5</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;">3</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;">4</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;">2</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</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;">7}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC29" 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 class="c1" style="color: #999988; font-style: italic;">2</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;">3</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;">4</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;">6</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;">3</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 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;">4</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;">5</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;">3</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;"> 1</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;">3</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 9</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 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;">5</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;">3</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;">2</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;">3</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;">3</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">5</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;">2</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 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;">7}</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC30" 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 class="c1" style="color: #999988; font-style: italic;">4</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;">5</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;">5</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;">6</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;">5</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;">6</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;">6</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;">5</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;">3</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 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 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;">6</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 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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">6</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;">4</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;">4</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;"> 1</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;">3</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;">6</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;">6</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;">3</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;">7}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC31" 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 class="c1" style="color: #999988; font-style: italic;">2</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;">4</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;">4</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;">3</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;">5</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;">3</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;">3</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;">4</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;">4</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;">5</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;">5</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;">2</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;">5</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;">6</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 9</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;">2</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;">3</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;">6</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;">5</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;">4</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;">4</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;">3</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;">4</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;">7}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC32" class="line" lang="brainfuck"><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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</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;"> </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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</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 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 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;">2</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;">2</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;">5</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;">5</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 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;">3</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;">4</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;">2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 7</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">5</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;">3</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;">4</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 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 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;">2</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;">7}</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC33" 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 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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">3</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 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;">3</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;">2</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;">2</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;">2</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;">4</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;">4</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;">2</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;">3</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;">2</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;">2</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;">4</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;">3</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;"> 7</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;">4</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;">3</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 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;">2</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;">2</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;">2</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;">7}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC34" 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 class="c1" style="color: #999988; font-style: italic;">5</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;">5</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;">7</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;">7</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;">4</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;">3</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;">5</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;">4</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;">5</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;">5</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;">3</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;">5</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;">3</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">6</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;">5</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;">4</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 12</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">6</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;">7</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;">4</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;">4</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;">7}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
35
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC35" 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 class="c1" style="color: #999988; font-style: italic;">3</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;">3</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;">4</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;">6</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;">4</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;">3</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;">4</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;">5</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">3</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;">3</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;">3</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;">3</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">5</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;">3</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;">3</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;"> 9</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;">3</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;">5</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;">3</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;">2</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;">7}</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC36" 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 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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">5</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;">5</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;">6</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;">2</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;">4</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;">4</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;">6</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;">6</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 2</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">4</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">3</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;">4</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;">4</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 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;">6</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;">3</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 6</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;">6</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;">4</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;">2</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;">7}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC37" 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 class="c1" style="color: #999988; font-style: italic;">4</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;">3</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 6</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 6</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;">5</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 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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</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 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;">5</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;">6</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;">2</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;">5</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;">6</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;">4</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 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;">2</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;">7</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;">5</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;">6</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 7</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 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;">3</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;">7}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
38
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC38" 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 class="c1" style="color: #999988; font-style: italic;">2</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 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;">2</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">6</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 6</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 6</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;">4</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 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;">6</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;">5</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;"> </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">2</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;">6</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;">3</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 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;">2</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;">4</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;">3</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;">4</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 class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 7</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;">2</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;">7}</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC39" 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 class="c1" style="color: #999988; font-style: italic;">2</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;">2</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;">2</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;">3</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;">4</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;">2</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;">2</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;">4</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;">3</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;">2</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;">2</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;">2</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 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;">3</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;">4</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;">2</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;">2</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;">4</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;">2</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;">2</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;">3</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;">2</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;">2</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;">7}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC40" 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 class="c1" style="color: #999988; font-style: italic;">7</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;">7</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;">7</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;">7</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;">7</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;">7</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;">7</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;">7</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;">7</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;">7</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;">7</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;">7</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;">7</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;">7</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;">7</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;">7</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;">7</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;">7</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;">7</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;">7</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;">7</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;">7</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;">7</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 1}</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC41" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> };</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC42" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC43" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> max_score = Max (score_matrix</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">0);</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC44" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> penalty = Max (max_score</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;">Min (score_matrix</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">0));</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC45" class="line" lang="brainfuck"></span>
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46
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC46" class="line" lang="brainfuck"></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC47" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> options = {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
48
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC48" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "SEQ_ALIGN_CHARACTER_MAP" : "ACGTN"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
49
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC49" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "SEQ_ALIGN_GAP_OPEN" : 1</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">5*penalty</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
50
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC50" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "SEQ_ALIGN_GAP_OPEN2" : 1</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">5*penalty</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
51
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC51" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "SEQ_ALIGN_GAP_EXTEND" : 0</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">1*penalty</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
52
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC52" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "SEQ_ALIGN_GAP_EXTEND2" : 0</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">1*penalty</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
53
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC53" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "SEQ_ALIGN_FRAMESHIFT" : 2*penalty</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
54
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC54" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "SEQ_ALIGN_NO_TP" : 1</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
55
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC55" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "SEQ_ALIGN_AFFINE" : 1</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
56
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC56" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> "SEQ_ALIGN_CODON_ALIGN" : 1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="57" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
57
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC57" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> };</span></span>
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<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
58
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC58" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
59
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC59" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> base_frequencies = {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
60
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC60" class="line" lang="brainfuck"><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;">069352301}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
61
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC61" class="line" lang="brainfuck"><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;">021000333}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
62
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC62" class="line" lang="brainfuck"><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;">049862283}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
63
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><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;">026563029}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
64
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><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;">033026253}</span></span>
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65
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><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;">1054545}</span></span>
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66
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><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;">008970554}</span></span>
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67
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><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;">036648952}</span></span>
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68
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><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;">036329907}</span></span>
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69
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><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;">065164842}</span></span>
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70
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC70" class="line" lang="brainfuck"><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;">021805663}</span></span>
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71
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC71" class="line" lang="brainfuck"><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;">032992805}</span></span>
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72
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC72" class="line" lang="brainfuck"><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;">0348093}</span></span>
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73
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC73" class="line" lang="brainfuck"><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;">036818766}</span></span>
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74
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><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;">054168098}</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><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;">12149678}</span></span>
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76
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><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;">082464001}</span></span>
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77
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><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;">053564744}</span></span>
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78
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><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;">038383113}</span></span>
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79
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><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;">07112377}</span></span>
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80
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81
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82
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<td class="new_line diff-line-num new" data-linenumber="83" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
83
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC83" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
84
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC84" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> options</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"SEQ_ALIGN_SCORE_MATRIX"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = pSM2cSM(score_matrix</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "ACDEFGHIKLMNPQRSTVWY"</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> code</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"code"</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> code</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"ordering"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
85
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC85" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> shift_penalty = computeExpectedPerBaseScore (</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">5</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">score_matrix</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">base_frequencies);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
86
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC86" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
87
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC87" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _cdnaln_partialScoreMatrices = cSM2partialSMs(options</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"SEQ_ALIGN_SCORE_MATRIX"</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
88
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC88" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> {{shift_penalty__*1</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">5</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">shift_penalty__</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">shift_penalty__</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">shift_penalty*1</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">5}});</span></span>
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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
89
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC89" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
90
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC90" class="line" lang="brainfuck"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
91
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC91" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> options </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"SEQ_ALIGN_PARTIAL_3x1_SCORES"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = _cdnaln_partialScoreMatrices</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"3x1"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
92
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC92" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> options </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"SEQ_ALIGN_PARTIAL_3x2_SCORES"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = _cdnaln_partialScoreMatrices</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"3x2"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
93
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC93" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> options </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"SEQ_ALIGN_PARTIAL_3x4_SCORES"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = _cdnaln_partialScoreMatrices</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"3x4"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="94" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
94
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> options </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"SEQ_ALIGN_PARTIAL_3x5_SCORES"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = _cdnaln_partialScoreMatrices</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"3x5"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
95
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<td class="new_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
96
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> options </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"MATCH"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = computeExpectedPerBaseScore (1</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">score_matrix</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">base_frequencies);</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> options </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"E"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = Max (0</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;"> computeExpectedPerBaseScore (</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">4</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">score_matrix</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">base_frequencies));</span></span>
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98
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<td class="new_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
99
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 class="c1" style="color: #999988; font-style: italic;"> return options;</span></span>
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100
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
101
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<td class="new_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
102
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 class="c1" style="color: #999988; font-style: italic;"> lfunction cSM2partialSMs(_cdnScoreMatrix</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> penalties) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="104" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
104
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<td class="new_line diff-line-num new" data-linenumber="105" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
105
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> m3x5 = { 126</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 1250 };</span></span>
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<td class="new_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
106
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 class="c1" style="color: #999988; font-style: italic;"> m3x4 = { 126</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 500 };</span></span>
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<td class="new_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
107
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC107" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> m3x2 = { 126</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 75 };</span></span>
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<td class="new_line diff-line-num new" data-linenumber="108" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
108
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC108" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> m3x1 = { 126</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 15 };</span></span>
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<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
109
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC109" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="110" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
110
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC110" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
111
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC111" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (utility</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">Array1D (penalties) == 4) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="112" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
112
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC112" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> p3x1 = penalties </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>
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<td class="new_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
113
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC113" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> p3x2 = penalties </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;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
114
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC114" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> p3x4 = penalties </span><span class="p">[</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>
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<td class="new_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
115
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC115" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> p3x5 = penalties </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">3</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="116" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
116
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC116" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="117" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
117
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC117" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> p3x5 = 0;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
118
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC118" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> p3x4 = 0;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
119
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 class="c1" style="color: #999988; font-style: italic;"> p3x2 = 0;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
120
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> p3x1 = 0;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
121
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> }</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> for ( thisCodon = 0; thisCodon </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> 64; thisCodon </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1 ) {</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 ( d1 = 0; d1 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> 5; d1 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1 ) {</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> max100 = </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">1e100;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> max010 = </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">1e100;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> max001 = </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">1e100;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> for ( d2 = 0; d2 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> 5; d2 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1 ) {</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> partialCodon = 5 * d1 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> d2;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> max110 = </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">1e100;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> max101 = </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">1e100;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> max011 = </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">1e100;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> for ( d3 = 0; d3 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> 5; d3 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1 ) {</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> thisCodon2 = 5 * partialCodon </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> d3;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> thisScore = _cdnScoreMatrix</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon2 </span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> // this is the trivial and stupid way of doing it</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> but it should work</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> m3x5</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 10 * thisCodon2 </span><span class="nf" style="color: #990000; font-weight: 600;">+</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;"> = thisScore </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> p3x5;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> m3x5</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 10 * thisCodon2 </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;"> = thisScore </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> p3x5;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> m3x5</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 10 * thisCodon2 </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;"> = thisScore </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> p3x5;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> m3x5</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 10 * thisCodon2 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> 3 </span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = thisScore </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> p3x5;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> m3x5</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 10 * thisCodon2 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> 4 </span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = thisScore </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> p3x5;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> m3x5</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 10 * thisCodon2 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> 5 </span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = thisScore </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> p3x5;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
146
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> m3x5</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 10 * thisCodon2 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> 6 </span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = thisScore </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> p3x5;</span></span>
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<td class="new_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">
147
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> m3x5</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 10 * thisCodon2 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> 7 </span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = thisScore </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> p3x5;</span></span>
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148
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> m3x5</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 10 * thisCodon2 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> 8 </span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = thisScore </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> p3x5;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> m3x5</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 10 * thisCodon2 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> 9 </span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = thisScore </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> p3x5;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> m3x4</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 4 * thisCodon2 </span><span class="nf" style="color: #990000; font-weight: 600;">+</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;"> = thisScore </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> p3x4;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> m3x4</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 4 * thisCodon2 </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;"> = thisScore </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> p3x4;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> m3x4</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 4 * thisCodon2 </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;"> = thisScore </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> p3x4;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> m3x4</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 4 * thisCodon2 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> 3 </span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = thisScore </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> p3x4;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> // d1 is 1</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> max100 = Max( max100</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> _cdnScoreMatrix</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 25 * d1 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> 5 * d2 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> d3 </span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> );</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> max010 = Max( max010</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> _cdnScoreMatrix</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 25 * d2 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> 5 * d1 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> d3 </span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> );</span></span>
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<td class="new_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
159
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> max001 = Max( max001</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> _cdnScoreMatrix</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 25 * d2 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> 5 * d3 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> d1 </span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> );</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> // d1 and d2 are 1</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> max110 = Max( max110</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> _cdnScoreMatrix</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 25 * d1 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> 5 * d2 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> d3 </span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> );</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> max101 = Max( max101</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> _cdnScoreMatrix</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 25 * d1 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> 5 * d3 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> d2 </span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> );</span></span>
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<td class="new_line diff-line-num new" data-linenumber="164" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
164
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> max011 = Max( max011</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> _cdnScoreMatrix</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 25 * d3 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> 5 * d1 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> d2 </span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> );</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> }</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> m3x2</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 3 * partialCodon </span><span class="nf" style="color: #990000; font-weight: 600;">+</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;"> = max110 </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> p3x2;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> m3x2</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 3 * partialCodon </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;"> = max101 </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> p3x2;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> m3x2</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 3 * partialCodon </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;"> = max011 </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> p3x2;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> }</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<td class="new_line diff-line-num new" data-linenumber="172" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
172
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> m3x1</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 3 * d1 </span><span class="nf" style="color: #990000; font-weight: 600;">+</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;"> = max100 </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> p3x1;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> m3x1</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 3 * d1 </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;"> = max010 </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> p3x1;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> m3x1</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> thisCodon </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> 3 * d1 </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;"> = max001 </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> p3x1;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> }</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> return { "3x1": m3x1</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "3x2": m3x2</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "3x4": m3x4</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "3x5": m3x5 };</span></span>
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<td class="new_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
180
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> }</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<td class="new_line diff-line-num new" data-linenumber="182" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
182
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<td class="new_line diff-line-num new" data-linenumber="183" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
183
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> lfunction _digits (index) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="185" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
185
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> return {{index__$25</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> index__ % 25 $ 5</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> index__ % 5}};</span></span>
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<td class="new_line diff-line-num new" data-linenumber="186" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
186
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<td class="new_line diff-line-num new" data-linenumber="187" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
187
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> lfunction _hazN (digits) {</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 class="c1" style="color: #999988; font-style: italic;"> return digits </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;"> == 4 || digits </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;"> == 4 || digits </span><span class="p">[</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;"> == 4;</span></span>
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<td class="new_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">
190
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> };</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> lfunction _map_to_nuc (digits) {</span></span>
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<td class="new_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">
193
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> return digits </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;"> * 16 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> digits </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;"> * 4 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> digits</span><span class="p">[</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>
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<td class="new_line diff-line-num new" data-linenumber="194" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
194
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 class="c1" style="color: #999988; font-style: italic;"> };</span></span>
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<td class="new_line diff-line-num new" data-linenumber="195" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
195
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<td class="new_line diff-line-num new" data-linenumber="196" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
196
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> lfunction _generate_resolutions (digits) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="197" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
197
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> resolutions = {};</span></span>
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<td class="new_line diff-line-num new" data-linenumber="198" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
198
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 class="c1" style="color: #999988; font-style: italic;"> for (k = 0; k </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> 4; k </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
199
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> try = digits;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="200" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
200
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> if (digits</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;"> == 4) {</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> try </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;"> = k;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="202" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
202
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="203" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
203
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> for (k2 = 0; k2 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> 4; k2 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1) {</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 (digits</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;"> == 4) {</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> try </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;"> = k;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> }</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> for (k3 = 0; k3 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> 4; k3 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1) {</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> if (digits</span><span class="p">[</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;"> == 4) {</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> try </span><span class="p">[</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;"> = k;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> resolutions</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">_map_to_nuc (try)</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = 1;</span></span>
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212
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> }</span></span>
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213
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> }</span></span>
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214
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<td class="new_line diff-line-num new" data-linenumber="215" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
215
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> return Rows(resolutions);</span></span>
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216
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<td class="new_line diff-line-num new" data-linenumber="217" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
217
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<td class="new_line diff-line-num new" data-linenumber="218" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
218
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC218" 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 class="c1" style="color: #999988; font-style: italic;"> //</span></span>
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219
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC219" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="220" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
220
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC220" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> lfunction pSM2cSM (_scorematrix</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> _letters</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> code</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> ordering) {</span></span>
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221
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC221" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="222" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
222
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC222" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _cdnScoreMatrix = { 126 </span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 126 };</span></span>
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<td class="new_line diff-line-num new" data-linenumber="223" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
223
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC223" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _mapping = utility</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MapStrings ( ordering</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> _letters );</span></span>
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224
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC224" class="line" lang="brainfuck"></span>
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225
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC225" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="226" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
226
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC226" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for ( _k = 0; _k </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> 125; _k </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1 ) {</span></span>
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227
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC227" class="line" lang="brainfuck"></span>
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228
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC228" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> letters1 = _digits (_k);</span></span>
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229
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC229" class="line" lang="brainfuck"></span>
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230
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC230" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (_hazN (letters1)) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="231" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
231
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC231" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> letters1 = _generate_resolutions (letters1);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="232" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
232
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC232" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for ( _k2 = _k; _k2 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> 125 ; _k2 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1 ) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="233" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
233
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC233" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> letters2 = _digits (_k2);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="234" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
234
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC234" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (_hazN (letters2) == 0) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="235" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
235
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC235" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon2 = _map_to_nuc(letters2);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="236" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
236
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _mappedK2 = _mapping</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> code</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> codon2 </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;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="237" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
237
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _aScore = </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">1e4;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="238" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
238
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (_mappedK2 </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;">= 0) {</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_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">
240
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> res_count = utility</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">Array1D (letters1);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="241" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
241
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (r = 0; r </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> res_count; r </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="242" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
242
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> resolution_codon = 0 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> letters1</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">r</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="243" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
243
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC243" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> resolution_aa = _mapping</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> code</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> resolution_codon </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;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
244
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC244" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (resolution_aa </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;">= 0) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="245" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
245
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC245" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> try_score = _scorematrix</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> resolution_aa </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> _mappedK2 </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;"> 1;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="246" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
246
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC246" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (resolution_aa == _mappedK2 && codon2 != resolution_codon) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="247" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
247
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC247" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> try_score = try_score </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> 1;</span></span>
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248
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC248" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="249" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
249
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC249" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _aScore = Max (_aScore</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> try_score);</span></span>
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250
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC250" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="251" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
251
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC251" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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252
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC252" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="253" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
253
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC253" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="254" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
254
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC254" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="255" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
255
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC255" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _cdnScoreMatrix</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;"> _k2 </span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = _aScore;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
256
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC256" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _cdnScoreMatrix</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> _k2 </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;"> = _aScore;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="257" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
257
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC257" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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258
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC258" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="259" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
259
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC259" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="260" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
260
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC260" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon1 = _map_to_nuc(letters1);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="261" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
261
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC261" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
262
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC262" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _mappedK = _mapping</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> code</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> codon1 </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;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="263" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
263
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC263" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="264" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
264
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC264" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if ( _mappedK </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;">= 0) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="265" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
265
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC265" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for ( _k2 = _k; _k2 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> 125 ; _k2 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1 ) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="266" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
266
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC266" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> letters2 = _digits (_k2);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="267" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
267
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC267" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="268" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
268
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC268" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (_hazN (letters2)) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="269" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
269
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC269" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _aScore = </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">1e4;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="270" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
270
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC270" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> letters2 = _generate_resolutions (letters2);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="271" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
271
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC271" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> res_count = utility</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">Array1D (letters2);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="272" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
272
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC272" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (r = 0; r </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> res_count; r </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="273" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
273
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC273" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> resolution_codon = 0 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> letters2</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">r</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="274" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
274
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC274" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> resolution_aa = _mapping</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> code</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> resolution_codon </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;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="275" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
275
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC275" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (resolution_aa </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;">= 0) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="276" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
276
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC276" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> try_score = _scorematrix</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> _mappedK </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> resolution_aa </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;"> 1;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="277" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
277
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC277" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (resolution_aa == _mappedK && codon1 != resolution_codon) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="278" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
278
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC278" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> try_score = try_score </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> 1;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="279" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
279
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC279" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="280" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
280
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC280" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _aScore = Max (_aScore</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> try_score);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="281" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
281
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC281" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="282" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
282
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC282" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="283" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
283
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC283" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _cdnScoreMatrix</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;"> _k2 </span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = _aScore;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="284" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
284
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _cdnScoreMatrix</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> _k2 </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;"> = _aScore;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="285" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
285
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> continue;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="286" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
286
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon2 = _map_to_nuc(letters2);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="289" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
289
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="290" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
290
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _mappedK2 = _mapping</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> code</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> codon2 </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;">;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if ( _mappedK2 </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;">= 0 ) {</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _aScore = _scorematrix</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> _mappedK </span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;"> _mappedK2 </span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_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">
293
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if ( _mappedK == _mappedK2 && _k2 </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> _k ) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="294" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
294
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _aScore = _aScore </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> 1; // synonymous match</span></span>
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<td class="new_line diff-line-num new" data-linenumber="295" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
295
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="296" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
296
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC296" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="297" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
297
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> // stop codons don't match anything</span></span>
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<td class="new_line diff-line-num new" data-linenumber="298" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
298
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _aScore = </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">1e4;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="299" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
299
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _cdnScoreMatrix</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;"> _k2 </span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = _aScore;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _cdnScoreMatrix</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> _k2 </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;"> = _aScore;</span></span>
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<td class="new_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">
302
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else { // stop codons here</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for ( _k2 = _k; _k2 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> 125; _k2 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1 ) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="305" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
305
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> letters2 = _digits (_k2);</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (_hazN (letters2)) {</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> continue;</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="311" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
311
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="312" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
312
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> codon2 = _map_to_nuc(letters2);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="313" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
313
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="314" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
314
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC314" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _mappedK2 = _mapping</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> code</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> codon2 </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;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="315" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
315
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC315" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="316" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
316
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC316" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if ( _mappedK2 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> 0 ) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="317" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
317
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC317" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> // don't penalize stop codons matching themselves</span></span>
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<td class="new_line diff-line-num new" data-linenumber="318" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
318
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC318" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _cdnScoreMatrix</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;"> _k2 </span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = 0;</span></span>
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319
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC319" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _cdnScoreMatrix</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> _k2 </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;"> = 0;</span></span>
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320
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC320" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="321" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
321
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC321" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _cdnScoreMatrix</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;"> _k2 </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;">1e4;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="322" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
322
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC322" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _cdnScoreMatrix</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;"> _k2 </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;"> = </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">1e4;</span></span>
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323
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC323" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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324
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC324" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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325
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC325" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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326
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC326" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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327
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC327" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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328
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC328" class="line" lang="brainfuck"></span>
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329
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC329" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return _cdnScoreMatrix;</span></span>
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330
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC330" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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331
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC331" class="line" lang="brainfuck"></span>
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332
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC332" 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 class="c1" style="color: #999988; font-style: italic;"> //</span></span>
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333
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC333" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="334" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
334
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC334" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> lfunction computeExpectedPerBaseScore( _expectedIdentity</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> _cdnaln_scorematrix</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> _cdnaln_base_freqs ) {</span></span>
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335
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC335" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> meanScore = 0;</span></span>
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336
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC336" class="line" lang="brainfuck"></span>
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337
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC337" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (_aa1 = 0; _aa1 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> 20; _aa1 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="338" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
338
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC338" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (_aa2 = 0; _aa2 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> 20; _aa2 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
339
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC339" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if ( _aa1 != _aa2 ) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="340" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
340
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC340" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> meanScore </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;"> _expectedIdentity ) * _cdnaln_scorematrix</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">_aa1</span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;">_aa2</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> * _cdnaln_base_freqs</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">_aa1</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> * _cdnaln_base_freqs</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">_aa2</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="341" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
341
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC341" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="342" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
342
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC342" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> meanScore </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= _expectedIdentity * _cdnaln_scorematrix</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">_aa1</span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;">_aa1</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> * _cdnaln_base_freqs</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">_aa1</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> * _cdnaln_base_freqs</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">_aa1</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="343" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
343
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC343" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
344
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC344" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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345
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC345" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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346
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC346" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="347" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
347
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC347" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return meanScore;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="348" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
348
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC348" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="349" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
349
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC349" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="350" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
350
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC350" 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 class="c1" style="color: #999988; font-style: italic;"> //</span></span>
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<td class="new_line diff-line-num new" data-linenumber="351" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
351
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC351" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="352" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
352
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC352" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> lfunction computeCorrection (str) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="353" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
353
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC353" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> result = {1</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2};</span></span>
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354
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC354" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="355" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
355
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC355" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> result</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;"> = (str$"^\\</span><span class="nf" style="color: #990000; font-weight: 600;">-+</span><span class="c1" style="color: #999988; font-style: italic;">")</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">1</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">1;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
356
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC356" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> result</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = (str$"\\</span><span class="nf" style="color: #990000; font-weight: 600;">-+</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>
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<td class="new_line diff-line-num new" data-linenumber="357" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
357
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC357" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="358" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
358
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC358" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (result</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;"> </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;">= 0) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="359" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
359
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC359" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> result</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;"> = Abs(str)</span><span class="nf" style="color: #990000; font-weight: 600;">-</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;">1</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="360" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
360
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC360" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="361" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
361
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC361" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> else {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="362" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
362
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC362" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> result</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>
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<td class="new_line diff-line-num new" data-linenumber="363" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
363
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC363" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="364" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
364
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC364" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return result;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="365" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
365
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC365" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="366" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
366
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC366" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="367" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
367
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC367" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
368
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC368" 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 class="c1" style="color: #999988; font-style: italic;"> //</span></span>
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<td class="new_line diff-line-num new" data-linenumber="369" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
369
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC369" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="370" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
370
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC370" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> lfunction igg_alignment_cleanup (reference</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> query</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> offset_nuc</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> code) {</span></span>
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371
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC371" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="372" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
372
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC372" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> too_short = 0;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="373" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
373
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC373" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> too_long = 0;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="374" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
374
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC374" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> span = 0; // how many nucleotides in the reference were covered by non</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">gaps</span></span>
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<td class="new_line diff-line-num new" data-linenumber="375" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
375
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC375" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _seqL = Abs (reference);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="376" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
376
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC376" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="377" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
377
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC377" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="378" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
378
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC378" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> ref_cleaned = ""; ref_cleaned * 128;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="379" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
379
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC379" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> qry_cleaned = ""; qry_cleaned * 128;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="380" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
380
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC380" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="381" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
381
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC381" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _codon_in_reference = 0;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="382" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
382
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC382" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="383" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
383
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC383" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for ( _rcidx = 0; _rcidx </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> _seqL; _rcidx </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1 ) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="384" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
384
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC384" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _del1 = reference </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">_rcidx</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> != (reference </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">_rcidx</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">&&1);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="385" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
385
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC385" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (_del1) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="386" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
386
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC386" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> too_short </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="387" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
387
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC387" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _codon_in_reference </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="388" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
388
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC388" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> ref_cleaned * (reference </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">_rcidx</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">&&1);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="389" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
389
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC389" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> qry_cleaned * (query </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">_rcidx</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">&&1);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="390" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
390
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC390" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="391" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
391
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC391" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _del1 = query </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">_rcidx</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> != (query </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">_rcidx</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">&&1);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="392" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
392
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC392" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (_del1) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="393" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
393
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC393" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (_seqL</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">_rcidx </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> 3 && _codon_in_reference % 3 == 0) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="394" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
394
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC394" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> break;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="395" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
395
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC395" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="396" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
396
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC396" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> too_long </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="397" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
397
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC397" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="398" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
398
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC398" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> ref_cleaned * (reference </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">_rcidx</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">&&1);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="399" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
399
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC399" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> qry_cleaned * (query </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">_rcidx</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">&&1);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
400
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC400" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> span </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="401" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
401
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC401" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> _codon_in_reference </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">=1;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="402" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
402
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC402" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="403" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
403
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC403" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="404" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
404
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC404" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="405" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
405
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC405" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> ref_cleaned * 0; qry_cleaned * 0;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="406" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
406
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC406" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="407" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
407
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC407" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return {"REF": ref_cleaned</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "QRY": qry_cleaned</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "TOO_SHORT" : too_short</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "TOO_LONG": too_long</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "SPAN": span</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "OFFSET_AA" : offset_nuc$3 </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> (offset_nuc % 3 </span><span class="nb" style="color: #0086b3;">></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;">"OFFSET" : offset_nuc</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "AA" : alignments</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">TranslateCodonsToAminoAcids (qry_cleaned</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> (3</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">offset_nuc%3)%3</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> code)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "AA_REF" : alignments</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">TranslateCodonsToAminoAcids (ref_cleaned</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> (3</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">offset_nuc%3)%3</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> code)};</span></span>
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<td class="new_line diff-line-num new" data-linenumber="408" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
408
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC408" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="409" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
409
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC409" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
410
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC410" 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 class="c1" style="color: #999988; font-style: italic;"> //</span></span>
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<td class="new_line diff-line-num new" data-linenumber="411" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
411
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC411" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="412" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
412
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC412" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> lfunction correctReadUsingCodonAlignedData (ref</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> qry</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> code) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="413" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
413
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC413" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> reference_shifts = computeCorrection(ref);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="414" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
414
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC414" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="415" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
415
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC415" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> /*reference_shifts is the starting</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">ending nucleotide on the reference relative to the read</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;"> if reference is longer than the read</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> then both are 0*/</span></span>
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416
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC416" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="417" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
417
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC417" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> offsetFrom = (qry$"^\\</span><span class="nf" style="color: #990000; font-weight: 600;">-+</span><span class="c1" style="color: #999988; font-style: italic;">")</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">1</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>
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<td class="new_line diff-line-num new" data-linenumber="418" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
418
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC418" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> offsetTo = (qry$"\\</span><span class="nf" style="color: #990000; font-weight: 600;">-+</span><span class="c1" style="color: #999988; font-style: italic;">$")</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">0</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">1;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="419" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
419
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC419" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="420" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
420
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC420" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> /* the $ looks for the regular expression in bestAl</span><span class="p">[</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;"> and returns a 2x1 array with the starting and ending 0</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">based positions of the regular expression</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;"> in this case multiple indels</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;"> returns </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">1 for both if the regular expression is not found</span><span class="nf" style="color: #990000; font-weight: 600;">.</span></span>
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421
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC421" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> i</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">e</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;">based index leading indels start at (bestAl</span><span class="p">[</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;">$"^\\</span><span class="nf" style="color: #990000; font-weight: 600;">-+</span><span class="c1" style="color: #999988; font-style: italic;">")</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> and end at (bestAl</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">2</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">$"^\\</span><span class="nf" style="color: #990000; font-weight: 600;">-+</span><span class="c1" style="color: #999988; font-style: italic;">")</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;">; trailing indels start at (bestAl</span><span class="p">[</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;">$"\\</span><span class="nf" style="color: #990000; font-weight: 600;">-+</span><span class="c1" style="color: #999988; font-style: italic;">$")</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;"> and end at (bestAl</span><span class="p">[</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;">$"\\</span><span class="nf" style="color: #990000; font-weight: 600;">-+</span><span class="c1" style="color: #999988; font-style: italic;">$")</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>
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422
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC422" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="423" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
423
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC423" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> so offSetFrom to offSetTo will return the reference sequence co</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">ordinates overlapping with the read</span><span class="nf" style="color: #990000; font-weight: 600;">.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="424" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
424
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC424" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> */</span></span>
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425
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC425" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="426" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
426
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC426" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="427" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
427
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC427" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (offsetTo </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> 0) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="428" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
428
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC428" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> offsetTo = Abs(qry)</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">1; /*if no trailing indels then to end of read*/</span></span>
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429
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC429" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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430
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC430" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="431" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
431
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC431" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> // check to see if the prefix in REF has some out</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">of</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">frame indels so that we can start offsetFrom in the correct frame */</span></span>
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432
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC432" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="433" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
433
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC433" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (offsetFrom </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> 0) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="434" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
434
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC434" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> frame_skips = 0;</span></span>
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435
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC435" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (i = 0; i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> offsetFrom; i </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1) {</span></span>
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436
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC436" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if ((ref</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;"> && 1) != ref</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>
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437
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC437" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> frame_skips </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="438" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
438
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC438" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="439" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
439
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC439" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="440" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
440
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC440" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> offsetFrom </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;">frame_skips;</span></span>
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441
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC441" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="442" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
442
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC442" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="443" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
443
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC443" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> seqOffset = offsetFrom; /*set the offset of the read relative to the reference</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;"> ie the number of indels needed on the read to align to the reference */</span></span>
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<td class="new_line diff-line-num new" data-linenumber="444" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
444
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC444" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> offsetFrom </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= reference_shifts</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;">; /*if the read starts before the reference then shift to start of reference ie</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;"> by reference_shifts</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>
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<td class="new_line diff-line-num new" data-linenumber="445" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
445
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC445" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> offsetTo = offsetTo </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> reference_shifts</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;">; /*if the read extends beyond the reference then shift to end of reference ie</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;"> by reference_shifts</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;"> */</span></span>
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<td class="new_line diff-line-num new" data-linenumber="446" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
446
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC446" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="447" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
447
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC447" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> theSeq = qry;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="448" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
448
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC448" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> theSeq = qry</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">reference_shifts</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;">Abs(qry)</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">reference_shifts</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">1</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;">; /*the nucleotide sequence of the read that overlaps with the reference sequence */</span></span>
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<td class="new_line diff-line-num new" data-linenumber="449" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
449
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC449" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="450" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
450
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC450" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> nucSeq = qry</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">offsetFrom</span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;">offsetTo</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">; /*read sequence pruned to exactly overlapping region*/</span></span>
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<td class="new_line diff-line-num new" data-linenumber="451" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
451
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC451" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> nucSeqRef = ref</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">offsetFrom</span><span class="p">][</span><span class="c1" style="color: #999988; font-style: italic;">offsetTo</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">; /*reference sequence pruned to exactly overlapping region*/</span></span>
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<td class="new_line diff-line-num new" data-linenumber="452" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
452
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC452" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="453" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
453
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC453" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> extra_keys = {};</span></span>
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<td class="new_line diff-line-num new" data-linenumber="454" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
454
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC454" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="455" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
455
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC455" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (reference_shifts</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) { // 'qry' has a prefix that's not aligned to the reference</span></span>
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<td class="new_line diff-line-num new" data-linenumber="456" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
456
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC456" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> extra_keys</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">'PREFIX'</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = qry</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;">reference_shifts</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;">1</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="457" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
457
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC457" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="458" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
458
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC458" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (reference_shifts</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;"> </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> 0) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="459" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
459
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC459" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> l = Abs (qry);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="460" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
460
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC460" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> extra_keys</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">'SUFFIX'</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = qry</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">l</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">reference_shifts</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;">l</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>
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<td class="new_line diff-line-num new" data-linenumber="461" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
461
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC461" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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462
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC462" class="line" lang="brainfuck"></span>
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463
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC463" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="464" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
464
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC464" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return utility</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">Extend (igg_alignment_cleanup (nucSeqRef</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> nucSeq</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">seqOffset</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> code)</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> extra_keys);</span></span>
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465
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC465" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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466
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC466" class="line" lang="brainfuck"></span>
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467
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC467" class="line" lang="brainfuck"></span>
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468
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC468" 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 class="c1" style="color: #999988; font-style: italic;"> //</span></span>
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469
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC469" class="line" lang="brainfuck"></span>
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470
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC470" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="471" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
471
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC471" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> lfunction align_sequence_to_reference_set (seq</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> references</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> alignment_settings</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> seq_name) {</span></span>
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472
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC472" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="473" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
473
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC473" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="474" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
474
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC474" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> input = {1</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;">2};</span></span>
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<td class="new_line diff-line-num new" data-linenumber="475" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
475
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC475" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> input </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;"> = seq;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="476" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
476
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC476" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="477" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
477
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC477" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> overall = {'SCORE' : </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">1e100</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> 'REFNAME' : ''};</span></span>
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<td class="new_line diff-line-num new" data-linenumber="478" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
478
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC478" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="479" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
479
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC479" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (id</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> seq; in; references) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="480" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
480
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC480" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> input </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;"> = seq;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="481" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
481
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC481" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> AlignSequences (result</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> input</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> alignment_settings);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="482" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
482
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC482" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="483" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
483
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC483" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> result = result</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>
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<td class="new_line diff-line-num new" data-linenumber="484" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
484
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC484" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="485" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
485
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC485" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (result </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;">= overall</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">'SCORE'</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="486" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
486
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC486" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="487" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
487
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC487" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (alignment_settings </span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"REPORT_VARIANTS"</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;">0</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> == overall</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">'SCORE'</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> && Abs (overall</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">'REFNAME'</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">)) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="488" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
488
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC488" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> overall</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">'REFNAME'</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;"> id;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="489" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
489
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC489" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } else {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="490" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
490
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC490" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> overall</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">'REFNAME'</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> = id;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="491" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
491
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC491" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="492" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
492
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC492" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> overall</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">'SCORE'</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;">0</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="493" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
493
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC493" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> overall</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">'RAW</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">REF'</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;">1</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="494" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
494
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC494" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> overall</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">'RAW</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">QRY'</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;">2</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="495" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
495
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC495" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="496" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
496
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC496" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
497
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC497" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="498" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
498
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC498" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="499" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
499
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC499" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (Type (overall</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">'RAW</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">REF'</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">) == "String") {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="500" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
500
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC500" class="line" lang="brainfuck"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
501
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC501" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> computed_score = (overall</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"SCORE"</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;"> 30 * alignment_settings</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"MATCH"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> * Exp (</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">Abs(seq)/3) ) / Abs (seq) * 3 ;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="502" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
502
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC502" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="503" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
503
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC503" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (alignment_settings</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"E"</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;">= computed_score) {</span></span>
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504
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC504" 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;">Extend (overall</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> correctReadUsingCodonAlignedData (overall</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">'RAW</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">REF'</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> overall</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">'RAW</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">QRY'</span><span class="p">]</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> alignment_settings</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"code"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">));</span></span>
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505
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC505" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="506" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
506
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC506" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="507" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
507
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (alignment_settings</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"SEQ_ALIGN_CODON_ALIGN"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;"> == TRUE && overall</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"SPAN"</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;">= 3) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="508" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
508
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> //assert (0</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> "Internal error in align_sequence_to_reference_set" </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> overall </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> "\nComputed score `computed_score`; expected score " </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> alignment_settings</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"E"</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;"> "; match score " </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;"> alignment_settings</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"MATCH"</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;"> "\nInput sequence: `seq`");</span></span>
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<td class="new_line diff-line-num new" data-linenumber="509" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
509
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return None;</span></span>
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510
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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511
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return overall;</span></span>
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512
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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513
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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514
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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515
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"></span>
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516
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return None;</span></span>
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517
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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518
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
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519
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#3945e6db8feb0e4ed58719b69ff3d8485bc45e87"><strong style="font-weight: 600;">res/TemplateBatchFiles/libv3/tasks/trees.bf</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="436" style="width: 35px; 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="436" style="width: 35px; 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">@@ -436,6 +436,28 @@ lfunction trees.extract_paml_annotation (tree_string) {</td>
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436
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC436" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> return result;</span></span>
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437
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC437" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">}</span></span>
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438
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC438" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="439" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
439
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC439" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">/**</span></span>
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<td class="new_line diff-line-num new" data-linenumber="440" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
440
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC440" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> * @name trees</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">AdjustZerosToNearZeros</span></span>
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<td class="new_line diff-line-num new" data-linenumber="441" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
441
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC441" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> * Given a tree dict and a list of matching parameter estimates</span></span>
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<td class="old_line diff-line-num new" data-linenumber="439" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="442" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
442
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC442" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> * this traverses the estimates and converts terminal branch lengths that are exactly 0 to something small (1e</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">6)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="443" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
443
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC443" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> * internal branches removed and modifies in in place</span></span>
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444
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC444" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> * @param tree </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> dict of the tree object</span></span>
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445
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC445" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> * @param estimates </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;"> dict with branch length estimates</span></span>
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446
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC446" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> * @return nothing; estimates modified in place</span></span>
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447
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC447" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> */</span></span>
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448
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC448" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="449" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
449
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC449" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">lfunction trees</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">AdjustZerosToNearZeros (tree</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> estimates) {</span></span>
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450
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC450" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="451" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
451
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC451" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (branch</span><span class="nf" style="color: #990000; font-weight: 600;">,</span><span class="c1" style="color: #999988; font-style: italic;"> value; in; tree </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;">trees</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">partitioned"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="452" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
452
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC452" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (value != ^"terms</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">tree_attributes</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">internal") {</span></span>
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453
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC453" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if (estimates / branch) {</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC454" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> if ((estimates</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">branch</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;">fit</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MLE"</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;"> 1e</span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="c1" style="color: #999988; font-style: italic;">10) {</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC455" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> (estimates</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">branch</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;">fit</span><span class="nf" style="color: #990000; font-weight: 600;">.</span><span class="c1" style="color: #999988; font-style: italic;">MLE"</span><span class="p">]</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>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC457" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> } </span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC458" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC459" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC463" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;">/**</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="722" style="width: 35px; 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="744" style="width: 35px; 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">@@ -722,9 +744,10 @@ lfunction trees.ParsimonyLabel(tree_id, given_labels) {</td>
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722
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<td class="new_line diff-line-num" data-linenumber="744" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
744
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC744" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> scores = {}; // node name </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> score of optimal labeling staring at this now given parent state</span></span>
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<td class="old_line diff-line-num" data-linenumber="723" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
723
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<td class="new_line diff-line-num" data-linenumber="745" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
745
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC745" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> optimal_labeling = {}; // node name </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> current node labeling which achieves this score</span></span>
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724
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<td class="new_line diff-line-num" data-linenumber="746" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
746
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC746" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> resulting_labels = {}; // internal nodes </span><span class="nf" style="color: #990000; font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #999988; font-style: italic;"> label</span></span>
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725
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC725" class="line" lang="brainfuck"></span>
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747
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC747" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> </span></span>
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<td class="new_line diff-line-num" data-linenumber="748" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
748
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC748" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> // pass 1 to fill in the score matrix</span></span>
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727
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<td class="new_line diff-line-num" data-linenumber="749" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
749
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC749" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (k = 0; k </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> Abs (tree_avl) ; k </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1) {</span></span>
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750
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC750" 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 (node_name);</span></span>
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<td class="old_line diff-line-num" data-linenumber="728" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
728
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<td class="new_line diff-line-num" data-linenumber="751" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
751
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC751" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> node_name = (tree_avl</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;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"Name"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="729" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
729
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> node_children = (tree_avl</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;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"Children"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="730" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
730
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> c_count = Abs (node_children);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="811" style="width: 35px; 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">@@ -788,7 +811,7 @@ lfunction trees.ParsimonyLabel(tree_id, given_labels) {</td>
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788
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<td class="new_line diff-line-num" data-linenumber="811" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
811
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC811" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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789
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<td class="new_line diff-line-num" data-linenumber="812" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
812
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC812" class="line" lang="brainfuck"></span>
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<td class="old_line diff-line-num" data-linenumber="790" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
790
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<td class="new_line diff-line-num" data-linenumber="813" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
813
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC813" class="line" lang="brainfuck"></span>
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<td class="old_line diff-line-num old" data-linenumber="791" 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">
791
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<td class="new_line diff-line-num old" data-linenumber="814" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;"> // pass 2 to choose the best state for subtree parents</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="814" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
814
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC814" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span>// pass 2 to choose the best state for subtree parents</span></span>
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792
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<td class="new_line diff-line-num" data-linenumber="815" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
815
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC815" class="line" lang="brainfuck"></span>
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<td class="old_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
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816
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC816" class="line" lang="brainfuck"></span>
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<td class="old_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
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<td class="new_line diff-line-num" data-linenumber="817" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
817
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC817" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> total_score = 0;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="826" style="width: 35px; 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="849" style="width: 35px; 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">@@ -826,6 +849,8 @@ lfunction trees.ParsimonyLabel(tree_id, given_labels) {</td>
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<td class="old_line diff-line-num" data-linenumber="826" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
826
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<td class="new_line diff-line-num" data-linenumber="849" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
849
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC849" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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827
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<td class="new_line diff-line-num" data-linenumber="850" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
850
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC850" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> }</span></span>
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<td class="old_line diff-line-num" data-linenumber="828" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
828
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<td class="new_line diff-line-num" data-linenumber="851" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
851
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC851" class="line" lang="brainfuck"></span>
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<td class="new_line diff-line-num new" data-linenumber="852" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
852
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC852" 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 (labels);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="853" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
853
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC853" class="line" lang="brainfuck"></span>
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829
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<td class="new_line diff-line-num" data-linenumber="854" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
854
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC854" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> tree_avl = (^tree_id) ^ 1;</span></span>
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830
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<td class="new_line diff-line-num" data-linenumber="855" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
855
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC855" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> for (k = 2; k </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #999988; font-style: italic;"> Abs (tree_avl); k </span><span class="nf" style="color: #990000; font-weight: 600;">+</span><span class="c1" style="color: #999988; font-style: italic;">= 1) {</span></span>
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<td class="old_line diff-line-num" data-linenumber="831" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
831
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<td class="new_line diff-line-num" data-linenumber="856" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
856
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC856" class="line" lang="brainfuck"><span class="c1" style="color: #999988; font-style: italic;"> node_name = (tree_avl</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;">)</span><span class="p">[</span><span class="c1" style="color: #999988; font-style: italic;">"Name"</span><span class="p">]</span><span class="c1" style="color: #999988; font-style: italic;">;</span></span>
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<li id="e5a5cb83991ca482b4f0a3424fd55eea54f6d652">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#e5a5cb83991ca482b4f0a3424fd55eea54f6d652"><strong style="font-weight: 600;">src/core/fisher_exact.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" style="width: 35px; 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="18" style="width: 35px; 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">@@ -18,6 +18,7 @@ Function prototype is declared in matrix.h</td>
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<td class="old_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
18
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18
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC18" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
19
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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
19
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC19" class="line" lang="cpp"><span class="cm" style="color: #999988; font-style: italic;">*/</span></span>
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20
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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
20
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC20" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
21
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999999; font-weight: 600;">#include</span> <span class="cpf"><stdlib.h></span></span>
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21
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<td class="new_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
22
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999999; font-weight: 600;">#include</span> <span class="cpf"><math.h></span></span>
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22
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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
23
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC23" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
23
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<td class="new_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
24
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999999; font-weight: 600;">#include</span> <span class="cpf">"global_things.h"</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#07aceb8d215a75908cea626d9c80bc2a7c06639c"><strong style="font-weight: 600;">src/core/global_things.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="93" style="width: 35px; 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="93" style="width: 35px; 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">@@ -93,6 +93,7 @@ namespace hy_global {</td>
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<td class="old_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
93
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<td class="new_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
93
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC93" class="line" lang="cpp"> <span class="n" style="color: #333333;">has_terminal_stdout</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span></span>
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<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
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cpp"> <span class="n" style="color: #333333;">has_terminal_stderr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span></span>
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<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
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cpp"> <span class="n" style="color: #333333;">ignore_kw_defaults</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
96
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cpp"> <span class="n" style="color: #333333;">exiting_with_error</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span></span>
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<td class="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
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<td class="new_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
97
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cpp"> <span class="n" style="color: #333333;">force_verbosity_from_cli</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
97
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cpp"> </span>
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<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
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cpp"> <span class="n" style="color: #333333;">hyFile</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">hy_error_log_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span></span>
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<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="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">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -122,7 +123,7 @@ namespace hy_global {</td>
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122
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;">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>
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123
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;">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>
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<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
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<td class="new_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
125
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;">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>
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<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
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<td class="new_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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;">3</span>"</span><span class="p">),</span></span>
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<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">
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 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;">8</span>"</span><span class="p">),</span></span>
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<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
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<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
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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;">kNoneToken</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #dd1144;">"None"</span><span class="p">,</span></span>
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<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
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<td class="new_line diff-line-num" data-linenumber="129" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
129
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="745" style="width: 35px; 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="746" style="width: 35px; 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">@@ -745,6 +746,7 @@ namespace hy_global {</td>
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745
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<td class="new_line diff-line-num" data-linenumber="746" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
746
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC746" class="line" lang="cpp"> <span class="c1" style="color: #999988; font-style: italic;">//____________________________________________________________________________________</span></span>
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746
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<td class="new_line diff-line-num" data-linenumber="747" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
747
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC747" class="line" lang="cpp"> <span class="kt" style="color: #445588; font-weight: 600;">void</span> <span class="nf" style="color: #990000; font-weight: 600;">HandleApplicationError</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333333;">_String</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333333;">message</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">bool</span> <span class="n" style="color: #333333;">force_exit</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">bool</span> <span class="n" style="color: #333333;">dump_core</span><span class="p">)</span> <span class="p">{</span></span>
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747
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748
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC748" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" data-linenumber="749" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
749
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC749" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num" data-linenumber="748" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
748
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<td class="new_line diff-line-num" data-linenumber="750" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
750
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC750" 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;">force_exit</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333333;">currentExecutionList</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333333;">currentExecutionList</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">errorHandlingMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333333;">HY_BL_ERROR_HANDLING_SOFT</span><span class="p">)</span> <span class="p">{</span></span>
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749
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<td class="new_line diff-line-num" data-linenumber="751" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
751
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC751" class="line" lang="cpp"> <span class="n" style="color: #333333;">currentExecutionList</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">ReportAnExecutionError</span><span class="p">(</span><span class="n" style="color: #333333;">message</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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750
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="785" style="width: 35px; 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">@@ -785,9 +787,14 @@ namespace hy_global {</td>
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<td class="old_line diff-line-num" data-linenumber="785" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
785
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cpp"> <span class="cp" style="color: #999999; font-weight: 600;">#else</span></span>
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786
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788
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cpp"> <span class="n" style="color: #333333;">errMsg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">message</span><span class="p">;</span></span>
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787
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789
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cpp"> <span class="cp" style="color: #999999; font-weight: 600;">#endif</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">exiting_with_error</span><span class="p">)</span> <span class="p">{</span></span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cpp"> <span class="n" style="color: #333333;">errMsg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">errMsg</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;">An additional error occurred while handling the first error. Error messages may be incomplete</span><span class="se" style="color: #dd1144;">\n</span><span class="s" style="color: #dd1144;">"</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
792
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="793" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
793
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cpp"> <span class="n" style="color: #333333;">exiting_with_error</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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788
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cpp"> <span class="n" style="color: #333333;">errMsg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">ConstructAnErrorMessage</span> <span class="p">(</span><span class="n" style="color: #333333;">errMsg</span><span class="p">);</span></span>
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789
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<td class="new_line diff-line-num old" data-linenumber="795" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cpp"> <span class="n" style="color: #333333;">StringToConsole</span><span class="p">(</span><span class="n" style="color: #333333;">errMsg</span><span class="p">);</span></span>
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790
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<td class="new_line diff-line-num old" data-linenumber="795" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="cpp"> <span class="cp" style="color: #999999; font-weight: 600;">#endif </span></span>
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795
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC795" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="796" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
796
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC796" class="line" lang="cpp"> <span class="n" style="color: #333333;">StringToConsole</span><span class="p">(</span><span class="n" style="color: #333333;">errMsg</span><span class="p">);</span></span>
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797
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC797" class="line" lang="cpp"> <span class="cp" style="color: #999999; font-weight: 600;">#endif</span></span>
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<td class="new_line diff-line-num" data-linenumber="798" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
798
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC798" class="line" lang="cpp"> </span>
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792
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<td class="new_line diff-line-num" data-linenumber="799" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
799
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC799" class="line" lang="cpp"> <span class="cp" style="color: #999999; font-weight: 600;">#if defined __UNIX__</span></span>
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793
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800
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC800" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">hy_drop_into_debug_mode</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#2a8dd324ded753b0b3c559ac3950a2881ccd7a93"><strong style="font-weight: 600;">src/core/likefunc.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3105" style="width: 35px; 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="3105" style="width: 35px; 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">@@ -3105,7 +3105,7 @@ inline hyFloat sqr (hyFloat x)</td>
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3105
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<td class="new_line diff-line-num" data-linenumber="3105" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3105
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3105" 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;">eq_freqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">GetIthFrequencies</span><span class="p">(</span><span class="n" style="color: #333333;">partition_index</span><span class="p">);</span></span>
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3106
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<td class="new_line diff-line-num" data-linenumber="3106" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3106
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3106" class="line" lang="cpp"> <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;">tip_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">filter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">NumberSpecies</span><span class="p">();</span></span>
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3107
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3107
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3107" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="3108" 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">
3108
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<td class="new_line diff-line-num old" data-linenumber="3108" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3108" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">filter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">GetData</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">GetTT</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">IsStandardNucleotide</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333333;">filter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">IsNormalFilter</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333333;">tip_count</span><span class="o" style="font-weight: 600;"><span class="idiff left deletion" style="background-color: #fac5cd;"><</span></span><span class="mi" style="color: #009999;"><span class="idiff right deletion" style="background-color: #fac5cd;">15</span>0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333333;">eq_freqs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">IsIndependent</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3108" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3108
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3108" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">filter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">GetData</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">GetTT</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">IsStandardNucleotide</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333333;">filter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">IsNormalFilter</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333333;">tip_count</span><span class="idiff left 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="mi" style="color: #009999;"><span class="idiff right addition" style="background-color: #c7f0d2;">30</span>0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333333;">eq_freqs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">IsIndependent</span><span class="p">())</span> <span class="p">{</span></span>
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3109
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<td class="new_line diff-line-num" data-linenumber="3109" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3109
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3109" class="line" lang="cpp"> <span class="c1" style="color: #999988; font-style: italic;">// if not - use distance estimates</span></span>
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3110
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3110
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3110" class="line" lang="cpp"></span>
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3111
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3111
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3111" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333333;">IsDegenerate</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4341" style="width: 35px; 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="4341" style="width: 35px; 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">@@ -4341,15 +4341,6 @@ _Matrix* _LikelihoodFunction::Optimize (_AssociativeList const * options)</td>
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4341
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<td class="new_line diff-line-num" data-linenumber="4341" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4341
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4341" class="line" lang="cpp"> <span class="n" style="color: #333333;">_variables_changed_during_last_compute</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #990000; font-weight: 600;">_SimpleList</span> <span class="p">();</span></span>
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4342
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<td class="new_line diff-line-num" data-linenumber="4342" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4342
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4342" class="line" lang="cpp"> <span class="n" style="color: #333333;">variables_changed_during_last_compute</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #990000; font-weight: 600;">_AVLList</span> <span class="p">(</span><span class="n" style="color: #333333;">_variables_changed_during_last_compute</span><span class="p">);</span></span>
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4343
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4343
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4343" class="line" lang="cpp"></span>
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4344
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<td class="new_line diff-line-num old" data-linenumber="4344" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4344" class="line" lang="cpp"><span class="cp" style="color: #999999; font-weight: 600;">#ifdef __HYPHYMPI__</span></span>
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4345
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<td class="new_line diff-line-num old" data-linenumber="4344" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4345" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">hy_mpi_node_rank</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>
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<td class="old_line diff-line-num old" data-linenumber="4346" 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">
4346
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<td class="new_line diff-line-num old" data-linenumber="4344" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4346" class="line" lang="cpp"><span class="cp" style="color: #999999; font-weight: 600;">#endif</span></span>
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4347
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<td class="new_line diff-line-num old" data-linenumber="4344" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4347" class="line" lang="cpp"> <span class="n" style="color: #333333;">BenchmarkThreads</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="p">);</span></span>
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4348
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<td class="new_line diff-line-num old" data-linenumber="4344" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4348" class="line" lang="cpp"><span class="cp" style="color: #999999; font-weight: 600;">#ifdef __HYPHYMPI__</span></span>
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4349
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4349" class="line" lang="cpp"> <span class="p">}</span></span>
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4350
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4350" class="line" lang="cpp"> </span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4352" class="line" lang="cpp"><span class="cp" style="color: #999999; font-weight: 600;">#endif</span></span>
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4346
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4489" style="width: 35px; 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>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -4489,7 +4480,14 @@ _Matrix* _LikelihoodFunction::Optimize (_AssociativeList const * options)</td>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4492" class="line" lang="cpp"> </span>
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4483
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4483" class="line" lang="cpp"><span class="cp" style="color: #999999; font-weight: 600;">#ifdef __HYPHYMPI__</span></span>
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4484
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4484" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">hy_mpi_node_rank</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>
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4485
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4485" class="line" lang="cpp"><span class="cp" style="color: #999999; font-weight: 600;">#endif</span></span>
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4486
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4486" class="line" lang="cpp"> <span class="n" style="color: #333333;">BenchmarkThreads</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="p">);</span></span>
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4487
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4487" class="line" lang="cpp"><span class="cp" style="color: #999999; font-weight: 600;">#ifdef __HYPHYMPI__</span></span>
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4488
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4488" class="line" lang="cpp"> <span class="p">}</span></span>
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4489
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4489" class="line" lang="cpp"><span class="cp" style="color: #999999; font-weight: 600;">#endif</span></span>
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4490
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4491
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4491" class="line" lang="cpp"> <span class="n" style="color: #333333;">_OptimiztionProgress</span> <span class="n" style="color: #333333;">progress_tracker</span><span class="p">;</span></span>
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4494
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4492
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4492" class="line" lang="cpp"> <span class="c1" style="color: #999988; font-style: italic;">//checkParameter (optimizationMethod,optMethodP,4.0);</span></span>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -4604,11 +4602,12 @@ _Matrix* _LikelihoodFunction::Optimize (_AssociativeList const * options)</td>
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4602
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4602" class="line" lang="cpp"> </span>
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4605
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4603
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4603" class="line" lang="cpp"> <span class="n" style="color: #333333;">hyFloat</span> <span class="n" style="color: #333333;">grad_precision</span><span class="p">;</span></span>
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4606
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<td class="new_line diff-line-num" data-linenumber="4604" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4604
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4604" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">maxSoFar</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">INFINITY</span><span class="p">)</span> <span class="p">{</span></span>
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4607
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<td class="new_line diff-line-num old" data-linenumber="4605" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4607" class="line" lang="cpp"> <span class="n" style="color: #333333;">grad_precision</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">MIN</span> <span class="p">(</span><span class="mf" style="color: #009999;">1000.</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">maxSoFar</span> <span class="o" style="font-weight: 600;"><span class="idiff left deletion" style="background-color: #fac5cd;">/</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="mf" style="color: #009999;"><span class="idiff deletion" style="background-color: #fac5cd;">5</span>00<span class="idiff right deletion" style="background-color: #fac5cd;">.</span></span><span class="p">);</span></span>
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4605
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4605" class="line" lang="cpp"> <span class="n" style="color: #333333;">grad_precision</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">MIN</span> <span class="p">(</span><span class="mf" style="color: #009999;">1000.</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">maxSoFar</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">*</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="mf" style="color: #009999;"><span class="idiff addition" style="background-color: #c7f0d2;">0.</span>00<span class="idiff right addition" style="background-color: #c7f0d2;">2</span></span><span class="p">);</span></span>
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4608
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<td class="new_line diff-line-num" data-linenumber="4606" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4606
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4606" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4609
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<td class="new_line diff-line-num old" data-linenumber="4607" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4609" class="line" lang="cpp"> <span class="n" style="color: #333333;">grad_precision</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #009999;">0.005</span><span class="p">;</span></span>
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4607
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4607" class="line" lang="cpp"> <span class="n" style="color: #333333;">grad_precision</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #009999;">0.00<span class="idiff left right addition" style="background-color: #c7f0d2;">2</span>5</span><span class="p">;</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4608" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4610" class="line" lang="cpp"> </span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4611" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">gradientBlocks</span><span class="p">.</span><span class="n" style="color: #333333;">nonempty</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4612" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="p">;</span> <span class="n" style="color: #333333;">b</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">gradientBlocks</span><span class="p">.</span><span class="n" style="color: #333333;">lLength</span><span class="p">;</span> <span class="n" style="color: #333333;">b</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4613" 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;">this_block</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333333;">_SimpleList</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333333;">gradientBlocks</span><span class="p">(</span><span class="n" style="color: #333333;">b</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4930" style="width: 35px; 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>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -4930,7 +4929,7 @@ _Matrix* _LikelihoodFunction::Optimize (_AssociativeList const * options)</td>
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4929
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4929" class="line" lang="cpp"> <span class="n" style="color: #333333;">_Matrix</span> <span class="n" style="color: #333333;">bestMSoFar</span><span class="p">;</span></span>
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4931
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4930
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4930" class="line" lang="cpp"> <span class="n" style="color: #333333;">GetAllIndependent</span> <span class="p">(</span><span class="n" style="color: #333333;">bestMSoFar</span><span class="p">);</span></span>
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4932
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<td class="new_line diff-line-num" data-linenumber="4931" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4931
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4931" class="line" lang="cpp"> <span class="n" style="color: #333333;">hyFloat</span> <span class="n" style="color: #333333;">prec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">Minimum</span> <span class="p">(</span><span class="n" style="color: #333333;">diffs</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">],</span> <span class="n" style="color: #333333;">diffs</span><span class="p">[</span><span class="mi" style="color: #009999;">1</span><span class="p">]),</span></span>
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4933
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<td class="new_line diff-line-num old" data-linenumber="4932" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4933" class="line" lang="cpp"> <span class="n" style="color: #333333;">grad_precision</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">Maximum</span><span class="p">(</span><span class="n" style="color: #333333;">diffs</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">],</span><span class="n" style="color: #333333;">diffs</span><span class="p">[</span><span class="mi" style="color: #009999;">1</span><span class="p">]);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="4932" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
4932
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4932" class="line" lang="cpp"> <span class="n" style="color: #333333;">grad_precision</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;"><span class="idiff left addition" style="background-color: #c7f0d2;">Maximum</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">precision</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;">Maximum</span><span class="p">(</span><span class="n" style="color: #333333;">diffs</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">],</span><span class="n" style="color: #333333;">diffs</span><span class="p">[</span><span class="mi" style="color: #009999;">1</span><span class="p">])<span class="idiff right addition" style="background-color: #c7f0d2;">)</span>;</span></span>
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4934
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4933
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4933" class="line" lang="cpp"></span>
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4935
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4934
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4934" class="line" lang="cpp"> <span class="n" style="color: #333333;">prec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">Minimum</span> <span class="p">(</span><span class="n" style="color: #333333;">Maximum</span> <span class="p">(</span><span class="n" style="color: #333333;">prec</span><span class="p">,</span> <span class="n" style="color: #333333;">precision</span><span class="p">),</span> <span class="mf" style="color: #009999;">1.</span><span class="p">);</span></span>
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4935
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5119" style="width: 35px; 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="5118" style="width: 35px; 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">@@ -5119,9 +5118,9 @@ _Matrix* _LikelihoodFunction::Optimize (_AssociativeList const * options)</td>
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5119
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<td class="new_line diff-line-num" data-linenumber="5118" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5118
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5118" class="line" lang="cpp"> <span class="c1" style="color: #999988; font-style: italic;">//verbosity_level = 101;</span></span>
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<td class="old_line diff-line-num" data-linenumber="5120" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5120
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<td class="new_line diff-line-num" data-linenumber="5119" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5119
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5119" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">use_adaptive_step</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="5121" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5121
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<td class="new_line diff-line-num" data-linenumber="5120" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5120
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">convergenceMode</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #009999;">2</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="5122" 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">
5122
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<td class="new_line diff-line-num old" data-linenumber="5121" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5122" class="line" lang="cpp"> <span class="n" style="color: #333333;">LocateTheBump</span> <span class="p">(</span><span class="n" style="color: #333333;">current_index</span><span class="p">,</span><span class="n" style="color: #333333;">precisionStep</span><span class="p">,</span> <span class="n" style="color: #333333;">maxSoFar</span><span class="p">,</span> <span class="n" style="color: #333333;">bestVal</span><span class="p">,</span> <span class="n" style="color: #333333;">go2Bound</span><span class="p">,</span> <span class="n" style="color: #333333;">precisionStep</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="5123" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="5121" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
5121
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5121" class="line" lang="cpp"> <span class="n" style="color: #333333;">LocateTheBump</span> <span class="p">(</span><span class="n" style="color: #333333;">current_index</span><span class="p">,</span><span class="n" style="color: #333333;">precisionStep</span><span class="p">,</span> <span class="n" style="color: #333333;">maxSoFar</span><span class="p">,</span> <span class="n" style="color: #333333;">bestVal</span><span class="p">,</span> <span class="n" style="color: #333333;">go2Bound</span><span class="p">,</span> <span class="n" style="color: #333333;">precisionStep</span><span class="idiff left 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="mf" style="color: #009999;"><span class="idiff right addition" style="background-color: #c7f0d2;">0.5</span></span><span class="p">);</span></span>
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5123
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<td class="new_line diff-line-num" data-linenumber="5122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5122
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5122" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="5124" 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">
5124
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<td class="new_line diff-line-num old" data-linenumber="5123" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5124" class="line" lang="cpp"> <span class="n" style="color: #333333;">LocateTheBump</span> <span class="p">(</span><span class="n" style="color: #333333;">current_index</span><span class="p">,</span><span class="n" style="color: #333333;">precisionStep</span><span class="p">,</span> <span class="n" style="color: #333333;">maxSoFar</span><span class="p">,</span> <span class="n" style="color: #333333;">bestVal</span><span class="p">,</span> <span class="n" style="color: #333333;">go2Bound</span><span class="p">,</span> <span class="n" style="color: #333333;"><span class="idiff left deletion" style="background-color: #fac5cd;">precisionStep</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 right deletion" style="background-color: #fac5cd;">//</span>convergenceMode == 2? precisionStep*0.25: precisionStep*0.0625);</span></span>
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5123
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5123" class="line" lang="cpp"> <span class="n" style="color: #333333;">LocateTheBump</span> <span class="p">(</span><span class="n" style="color: #333333;">current_index</span><span class="p">,</span><span class="n" style="color: #333333;">precisionStep</span><span class="p">,</span> <span class="n" style="color: #333333;">maxSoFar</span><span class="p">,</span> <span class="n" style="color: #333333;">bestVal</span><span class="p">,</span> <span class="n" style="color: #333333;">go2Bound</span><span class="p">,</span> <span class="n" style="color: #333333;">convergenceMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">2</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333333;">precisionStep</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #009999;">0.25</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333333;">precisionStep</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #009999;">0.0625</span><span class="p">);</span></span>
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5125
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5124
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5124" class="line" lang="cpp"> <span class="p">}</span></span>
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5126
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5125
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5125" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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5127
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<td class="new_line diff-line-num" data-linenumber="5126" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5126
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5126" class="line" lang="cpp"> <span class="n" style="color: #333333;">LocateTheBump</span> <span class="p">(</span><span class="n" style="color: #333333;">current_index</span><span class="p">,</span><span class="n" style="color: #333333;">brackStep</span><span class="p">,</span> <span class="n" style="color: #333333;">maxSoFar</span><span class="p">,</span> <span class="n" style="color: #333333;">bestVal</span><span class="p">,</span> <span class="n" style="color: #333333;">go2Bound</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6516" style="width: 35px; 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="6515" style="width: 35px; 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">@@ -6516,7 +6515,7 @@ void _LikelihoodFunction::ComputeGradient (_Matrix& gradient, hyFloat& gradi</td>
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<td class="old_line diff-line-num" data-linenumber="6516" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6516
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<td class="new_line diff-line-num" data-linenumber="6515" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6515
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6515" class="line" lang="cpp"> <span class="n" style="color: #333333;">hyFloat</span> <span class="n" style="color: #333333;">currentValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">GetIthIndependent</span><span class="p">(</span><span class="n" style="color: #333333;">index</span><span class="p">),</span></span>
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<td class="old_line diff-line-num" data-linenumber="6517" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6517
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<td class="new_line diff-line-num" data-linenumber="6516" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6516
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6516" class="line" lang="cpp"> <span class="n" style="color: #333333;">ub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">GetIthIndependentBound</span><span class="p">(</span><span class="n" style="color: #333333;">index</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;">currentValue</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="6518" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6518
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<td class="new_line diff-line-num" data-linenumber="6517" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6517
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6517" class="line" lang="cpp"> <span class="n" style="color: #333333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">currentValue</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">GetIthIndependentBound</span><span class="p">(</span><span class="n" style="color: #333333;">index</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">),</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6519" 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">
6519
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<td class="new_line diff-line-num old" data-linenumber="6518" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6519" class="line" lang="cpp"> <span class="n" style="color: #333333;">testStep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">MAX</span><span class="p">(</span><span class="n" style="color: #333333;">currentValue</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">gradientStep</span><span class="p">,</span><span class="n" style="color: #333333;">gradientStep</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="6520" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="6518" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6518
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6518" class="line" lang="cpp"> <span class="n" style="color: #333333;">testStep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">MAX</span><span class="p">(</span><span class="n" style="color: #333333;"><span class="idiff left addition" style="background-color: #c7f0d2;">fabs</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333333;">currentValue</span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">)</span></span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">gradientStep</span><span class="p">,</span><span class="n" style="color: #333333;">gradientStep</span><span class="p">);</span></span>
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6520
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6519
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6519" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num" data-linenumber="6521" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6521
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6520
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6520" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num" data-linenumber="6522" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6522
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<td class="new_line diff-line-num" data-linenumber="6521" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6521
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6521" class="line" lang="cpp"> <span class="c1" style="color: #999988; font-style: italic;">//printf ("%ld %s %20.18g\n", index, GetIthIndependentName (index)->get_str(), currentValue);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6691" style="width: 35px; 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="6690" style="width: 35px; 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">@@ -6691,6 +6690,10 @@ hyFloat _LikelihoodFunction::ConjugateGradientDescent (hyFloat step_precision</td>
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6691
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<td class="new_line diff-line-num" data-linenumber="6690" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6690
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6690" class="line" lang="cpp"> </span>
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6692
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<td class="new_line diff-line-num" data-linenumber="6691" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6691
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6691" class="line" lang="cpp"> <span class="c1" style="color: #999988; font-style: italic;">//printf ("\n\n_LikelihoodFunction::ConjugateGradientDescent ==> %d (%lg)\n", usedCachedResults, maxSoFar);</span></span>
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6693
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6692
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6692" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num new" data-linenumber="6694" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="6693" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6693
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6693" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">maxSoFar</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">INFINITY</span><span class="p">)</span> <span class="p">{</span></span>
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6694
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6694" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">maxSoFar</span><span class="p">;</span></span>
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6695
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6695" class="line" lang="cpp"> <span class="p">}</span></span>
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6696
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6696" class="line" lang="cpp"> </span>
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6694
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<td class="new_line diff-line-num" data-linenumber="6697" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6697
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6697" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">min_improvement_to_contuinue</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #009999;">0.</span><span class="p">)</span> <span class="p">{</span></span>
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6695
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6698
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6698" class="line" lang="cpp"> <span class="n" style="color: #333333;">min_improvement_to_contuinue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">initial_value</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">min_improvement_to_contuinue</span><span class="p">;</span></span>
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6696
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6699
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6699" class="line" lang="cpp"> <span class="p">}</span></span>
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<li id="f56f32153875ab0b47e6f25f776693958c4d187b">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#f56f32153875ab0b47e6f25f776693958c4d187b"><strong style="font-weight: 600;">src/core/likefunc2.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1254" style="width: 35px; 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="1254" style="width: 35px; 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">@@ -1254,8 +1254,11 @@ hyFloat mapParameterToInverval (hyFloat in, char type, bool inverse) {</td>
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1254
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1254
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1254" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1255
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<td class="new_line diff-line-num" data-linenumber="1255" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1255
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1255" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333333;">_hyphyIntervalMapSqueeze</span><span class="p">:</span></span>
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1256
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<td class="new_line diff-line-num" data-linenumber="1256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1256
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1256" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">inverse</span><span class="p">)</span> <span class="p">{</span></span>
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1257
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<td class="new_line diff-line-num old" data-linenumber="1257" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1257" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">in</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="mf" style="color: #009999;">1.</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">in</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1257" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1257
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1257" class="line" lang="cpp"> <span class="n" style="color: #333333;">in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">in</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="mf" style="color: #009999;">1.</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">in</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1258" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1258
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1258" class="line" lang="cpp"> <span class="c1" style="color: #999988; font-style: italic;">//return in;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1259" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1259
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1259" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">in</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">in</span><span class="p">;</span></span>
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1258
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<td class="new_line diff-line-num" data-linenumber="1260" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1260
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1260" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1261" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1261
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1261" class="line" lang="cpp"> <span class="n" style="color: #333333;">in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">sqrt</span> <span class="p">(</span><span class="n" style="color: #333333;">in</span><span class="p">);</span></span>
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1259
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<td class="new_line diff-line-num" data-linenumber="1262" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1262
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1262" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">in</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="mf" style="color: #009999;">1.</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">in</span><span class="p">);</span></span>
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1260
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<td class="new_line diff-line-num" data-linenumber="1263" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1263
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1263" class="line" lang="cpp"> <span class="p">}</span></span>
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1264
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1264" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#81843dd3cf849d08e0f197d837dd373534c7c756"><strong style="font-weight: 600;">src/core/matrix.cpp</strong></a>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -72,8 +72,8 @@ _String MATRIX_AGREEMENT = "CONVERT_TO_POLYNOMIALS",</td>
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72
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC72" class="line" lang="cpp"></span>
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73
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73
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC73" class="line" lang="cpp"></span>
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<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
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">_Matrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333333;">precisionArg</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="75" 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">
75
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<td class="new_line diff-line-num old" data-linenumber="75" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">_Matrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333333;">storageIncrement</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;"><span class="idiff left right deletion" style="background-color: #fac5cd;">16</span></span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="76" 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">
76
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<td class="new_line diff-line-num old" data-linenumber="75" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">_Matrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333333;">switchThreshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">3<span class="idiff left right deletion" style="background-color: #fac5cd;">5</span></span><span class="p">;</span></span>
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<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">
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<td class="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
75
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">_Matrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333333;">storageIncrement</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;"><span class="idiff left right addition" style="background-color: #c7f0d2;">20</span></span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
76
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">_Matrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333333;">switchThreshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">3<span class="idiff left right addition" style="background-color: #c7f0d2;">0</span></span><span class="p">;</span></span>
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77
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77
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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>
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<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
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<td class="new_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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 class="n" style="color: #333333;">hyFloat</span> <span class="n" style="color: #333333;">_Matrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333333;">truncPrecision</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #009999;">1e-16</span><span class="p">;</span></span>
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79
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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 class="cp" style="color: #999999; font-weight: 600;">#define MatrixMemAllocate(X) MemAllocate(X, false, 64)</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#9f127084157a2a4e11faf03320db0541dbae15dc"><strong style="font-weight: 600;">src/core/tree_evaluator.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3519" style="width: 35px; 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="3519" style="width: 35px; 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">@@ -3519,8 +3519,12 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList</td>
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3519
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<td class="new_line diff-line-num" data-linenumber="3519" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3519
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3519" 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;">INFINITY</span><span class="p">;</span></span>
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3520
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<td class="new_line diff-line-num" data-linenumber="3520" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3520
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3520" class="line" lang="cpp"><span class="cp" style="color: #999999; font-weight: 600;">#pragma omp critical</span></span>
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3521
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<td class="new_line diff-line-num" data-linenumber="3521" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3521
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3521" class="line" lang="cpp"> <span class="p">{</span></span>
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3522
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<td class="new_line diff-line-num old" data-linenumber="3522" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3522" class="line" lang="cpp"> <span class="c1" style="color: #999988; font-style: italic;">//printf ("BAILING WITH INFINITY %ld / %ld (%ld)\n", siteID, siteOrdering.list_data[siteID], siteOrdering.lLength);</span></span>
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3522
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3522" class="line" lang="cpp"> <span class="c1" style="color: #999988; font-style: italic;">//printf ("BAILING WITH INFINITY %ld / %ld (%ld)<span class="idiff left addition" style="background-color: #c7f0d2;">; (%ld);</span>\n", siteID, siteOrdering.list_data[siteID], siteOrdering.lLength<span class="idiff right addition" style="background-color: #c7f0d2;">, theFilter->theMap .get(siteOrdering.list_data[siteID]*3)</span>);</span></span>
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3523
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3523
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3523" class="line" lang="cpp"> <span class="n" style="color: #333333;">hy_global</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333333;">ReportWarning</span> <span class="p">(</span><span class="n" style="color: #333333;">_String</span><span class="p">(</span><span class="s" style="color: #dd1144;">"Site "</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="mi" style="color: #009999;">1L</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">siteOrdering</span><span class="p">.</span><span class="n" style="color: #333333;">list_data</span><span class="p">[</span><span class="n" style="color: #333333;">siteID</span><span class="p">])</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #dd1144;">" evaluated to a 0 probability in ComputeTreeBlockByBranch"</span><span class="p">);</span></span>
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3524
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3524" class="line" lang="cpp"> <span class="cm" style="color: #999988; font-style: italic;">/*long lfID = -1;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3525" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3525
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3525" class="line" lang="cpp"><span class="cm" style="color: #999988; font-style: italic;"> IsLinkedToALF (lfID);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3526" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3526
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3526" class="line" lang="cpp"><span class="cm" style="color: #999988; font-style: italic;"> ((_LikelihoodFunction*)likeFuncList (lfID))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3527" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3527
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3527" class="line" lang="cpp"><span class="cm" style="color: #999988; font-style: italic;"> ->_TerminateAndDump (_String("Site ") & (1L+siteOrdering.list_data[siteID]) & " evaluated to a 0 probability in ComputeTreeBlockByBranch", true);*/</span></span>
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3524
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<td class="new_line diff-line-num" data-linenumber="3528" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3528
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3528" class="line" lang="cpp"> <span class="p">}</span></span>
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3525
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3529
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3529" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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3526
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3530
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3530" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#0a0fab4854abeb8613cb11cc93839e27fcd1462b"><strong style="font-weight: 600;">tests/hbltests/libv3/FEL.wbf</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" style="width: 35px; 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="3" style="width: 35px; 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">@@ -3,7 +3,7 @@ GetString (version, HYPHY_VERSION, 0);</td>
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3
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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3" class="line" lang="plaintext">if (+version >= 2.4) {</span>
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4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="plaintext"> LoadFunctionLibrary ("SelectionAnalyses/FEL.bf", </span>
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5
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5" class="line" lang="plaintext"> {"--code" : "Universal", "--alignment" : PATH_TO_CURRENT_BF + "data/CD2.nex"/*, </span>
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<td class="old_line diff-line-num old" data-linenumber="6" 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">
6
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<td class="new_line diff-line-num old" data-linenumber="6" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext"> "--<span class="idiff left deletion" style="background-color: #fac5cd;">branches</span>" : "<span class="idiff deletion" style="background-color: #fac5cd;">All</span>",<span class="idiff right deletion" style="background-color: #fac5cd;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext"> "--<span class="idiff left addition" style="background-color: #c7f0d2;">pvalue</span>" : "<span class="idiff right addition" style="background-color: #c7f0d2;">0.2</span>",</span>
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7
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext"> "--limit-to-sites" : "144", "--save-lf-for-sites" : "144"*/</span>
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8
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8
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext"> });</span>
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9
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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
9
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext">} else {</span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#36997e9895fbc5aa292a49ff1287846b86977d31"><strong style="font-weight: 600;">tests/hbltests/libv3/MEME.wbf</strong></a>
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1
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2
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2
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="plaintext"></span>
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3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="plaintext">p_cut = 0.05;</span>
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3
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4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="plaintext"></span>
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4
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5" class="line" lang="plaintext">if (+version >= 2.4) {</span>
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<td class="old_line diff-line-num old" data-linenumber="5" 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">
5
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<td class="new_line diff-line-num old" data-linenumber="6" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="plaintext"> LoadFunctionLibrary ("SelectionAnalyses/MEME.bf", {"--code" : "Universal", "--alignment" : PATH_TO_CURRENT_BF + "data/CD2.nex", "--branches" : "All"});</span>
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6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext"> LoadFunctionLibrary ("SelectionAnalyses/MEME.bf", {"--code" : "Universal", </span>
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext"> "--alignment" : PATH_TO_CURRENT_BF + "data/CD2.nex", </span>
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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
8
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext"> "--branches" : "All",</span>
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<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
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext"> "--pvalue" : "" + p_cut});</span>
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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext">} else {</span>
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7
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11
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext"> LoadFunctionLibrary ("SelectionAnalyses/MEME.bf", {"0" : "Universal", "1" : PATH_TO_CURRENT_BF + "data/CD2.nex", "2" : "All", "3" : "0.1"});</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="44" style="width: 35px; 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="48" style="width: 35px; 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">@@ -44,16 +48,27 @@ branches = (((meme.json["MLE"])["content"])["0"])[-1][7];</td>
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<td class="old_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
44
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<td class="new_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
48
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC48" class="line" lang="plaintext">| 149 | 1 | 0.000 | 1.968 | 1.000 | 5.229 | Yes, p = 0.0335 | 0 |</span>
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45
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<td class="new_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
49
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC49" class="line" lang="plaintext">| 174 | 1 | 0.737 | 25.356 | 0.176 | 3.851 | Yes, p = 0.0684 | 1 |</span>
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46
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<td class="new_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
50
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC50" class="line" lang="plaintext"></span>
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51
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC51" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
52
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC52" class="line" lang="plaintext">| Codon | Partition | alpha |non-syn rate (beta) distribution, rates : weights| LRT |Episodic selection detected?| # branches | List of most common codon substitutions at this site |</span>
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<td class="old_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
53
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC53" class="line" lang="plaintext">|:----------:|:----------:|:----------:|:-----------------------------------------------:|:----------:|:--------------------------:|:----------:|:---------------------------------------------------------------------:|</span>
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<td class="old_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
54
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC54" class="line" lang="plaintext">| 43 | 1 | 0.000 | 0.00/15.54 : 0.83/0.17 | 4.878 | Yes, p = 0.0402 | 1 | [1]CTg>AAg |</span>
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<td class="new_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
55
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC55" class="line" lang="plaintext">| 67 | 1 | 0.000 | 0.00/99.81 : 0.79/0.21 | 5.675 | Yes, p = 0.0266 | 1 | [1]TcC>AcT,TCc>GAc |</span>
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<td class="old_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
56
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC56" class="line" lang="plaintext">| 76 | 1 | 0.000 | 0.00/48.40 : 0.70/0.30 | 10.326 | Yes, p = 0.0025 | 2 | [1]aCc>aTc,aGA>aCC,AGa>CTa |</span>
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<td class="old_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="57" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
57
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC57" class="line" lang="plaintext">| 98 | 1 | 0.002 | 0.00/26.81 : 0.55/0.45 | 4.573 | Yes, p = 0.0470 | 0 | [1]aCa>aAa,aCa>aTa,ACA>GAC,Aca>Gca |</span>
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<td class="old_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
58
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC58" class="line" lang="plaintext">| 113 | 1 | 0.002 | 0.00/8.41 : 0.34/0.66 | 5.871 | Yes, p = 0.0241 | 2 | [1]Tac>Cac,tAc>tCc,TCc>AAc,TCc>GAc |</span>
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<td class="old_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
59
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC59" class="line" lang="plaintext">| 117 | 1 | 0.000 | 0.00/4.81 : 0.00/1.00 | 5.246 | Yes, p = 0.0332 | 0 | [2]aCc>aTc|[1]aCc>aGc,Acc>Ccc,Acc>Gcc |</span>
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<td class="old_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
60
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC60" class="line" lang="plaintext">| 149 | 1 | 0.000 | 0.00/4.71 : 0.00/1.00 | 5.229 | Yes, p = 0.0335 | 0 | [1]aCc>aAc,ACc>GTc,Gtc>Ctc,Gtc>Ttc |</span>
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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
61
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC61" class="line" lang="plaintext"></span>
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47
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<td class="new_line diff-line-num" data-linenumber="62" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
62
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC62" class="line" lang="plaintext">*/</span>
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48
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext"></span>
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<td class="old_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
49
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext"></span>
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<td class="old_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
50
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext">test.lrt_sum = 0;</span>
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<td class="old_line diff-line-num" data-linenumber="51" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
51
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<td class="new_line diff-line-num" data-linenumber="66" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
66
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext">test.branch_sum = 0;</span>
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<td class="old_line diff-line-num" data-linenumber="52" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
52
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext"></span>
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<td class="old_line diff-line-num old" data-linenumber="53" 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">
53
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<td class="new_line diff-line-num old" data-linenumber="68" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC53" class="line" lang="plaintext">test.expected_positives = utility.MatrixToDict({{<span class="idiff left deletion" style="background-color: #fac5cd;">9,34,43,55,6</span>4,67,76,<span class="idiff deletion" style="background-color: #fac5cd;">81,</span>98,113,117,1<span class="idiff right deletion" style="background-color: #fac5cd;">22,141,149,17</span>4}});</span>
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<td class="new_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">
68
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext">test.expected_positives = utility.MatrixToDict({{4<span class="idiff left addition" style="background-color: #c7f0d2;">3</span>,67,76,98,113,117,14<span class="idiff right addition" style="background-color: #c7f0d2;">9</span>}});</span>
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54
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext"></span>
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<td class="old_line diff-line-num" data-linenumber="55" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
55
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<td class="new_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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC70" class="line" lang="plaintext">function confirm_site (site, p, dict) {</span>
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<td class="old_line diff-line-num old" data-linenumber="56" 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">
56
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<td class="new_line diff-line-num old" data-linenumber="71" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC56" class="line" lang="plaintext"> if (p <= <span class="idiff left right deletion" style="background-color: #fac5cd;">0.1</span>) {</span>
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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
71
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC71" class="line" lang="plaintext"> if (p <= <span class="idiff left right addition" style="background-color: #c7f0d2;">p_cut</span>) {</span>
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57
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72
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC72" class="line" lang="plaintext"> if (dict/(site+1)) {</span>
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<td class="old_line diff-line-num" data-linenumber="58" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
58
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73
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC73" class="line" lang="plaintext"> test.lrt_sum += lrts[site];</span>
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59
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext"> test.branch_sum += branches[site];</span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="90" style="width: 35px; 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">@@ -75,7 +90,7 @@ utility.ForEachPair (p_values,"_index_", "_p_",</td>
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75
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<td class="new_line diff-line-num" data-linenumber="90" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
90
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC90" class="line" lang="plaintext"> ");</span>
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76
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<td class="new_line diff-line-num" data-linenumber="91" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
91
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC91" class="line" lang="plaintext"></span>
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<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
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<td class="new_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
92
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC92" class="line" lang="plaintext">assert (check_value (</span>
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<td class="old_line diff-line-num old" data-linenumber="78" 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">
78
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<td class="new_line diff-line-num old" data-linenumber="93" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext"> test.lrt_sum, <span class="idiff left right deletion" style="background-color: #fac5cd;">72.175</span>, 0.05), "More than 5% difference in cumulative LRT for positively selected sites");</span>
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<td class="old_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
93
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC93" class="line" lang="plaintext"> test.lrt_sum, <span class="idiff left right addition" style="background-color: #c7f0d2;">41.798</span>, 0.05), "More than 5% difference in cumulative LRT for positively selected sites");</span>
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<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
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext">assert (check_value (</span>
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<td class="old_line diff-line-num old" data-linenumber="80" 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">
80
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<td class="new_line diff-line-num old" data-linenumber="95" 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">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext"> test.branch_sum, <span class="idiff left right deletion" style="background-color: #fac5cd;">11</span>, 0.0001), "Incorrect total # of branches with high EBF");</span>
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<td class="old_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
95
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext"> test.branch_sum, <span class="idiff left right addition" style="background-color: #c7f0d2;">6</span>, 0.0001), "Incorrect total # of branches with high EBF");</span>
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81
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<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
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; 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="plaintext"> </span></pre></td>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a9fb370c1a0e1c94b8815f76f8fc463f00629066...cab2836da06a67c36d4d8e44d103577abde69da1#38b1bdf535ce982a4d66a98621e0b96b49c1ec64"><strong style="font-weight: 600;">tests/hbltests/libv3/algae-mtDNA.wbf</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; 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="14" style="width: 35px; 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">@@ -14,7 +14,7 @@ assert (check_value (</td>
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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14
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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14" class="line" lang="plaintext"> (fitter.results)["LogL"], -2345.80, 0.05), "Incorrect log-likelihood for the codon model");</span>
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15
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15
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
16
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<td class="new_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
16
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC16" class="line" lang="plaintext">assert (check_value (</span>
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<td class="old_line diff-line-num old" data-linenumber="17" 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">
17
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<td class="new_line diff-line-num old" data-linenumber="17" 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: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC17" class="line" lang="plaintext"> (((fitter.results)["global"])["non-synonymous/synonymous rate ratio"])["MLE"], 0.0040, 0.0<span class="idiff left right deletion" style="background-color: #fac5cd;">1</span>), "Incorrect dN/dS ratio");</span>
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<td class="old_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
17
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC17" class="line" lang="plaintext"> (((fitter.results)["global"])["non-synonymous/synonymous rate ratio"])["MLE"], 0.0040, 0.0<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span>), "Incorrect dN/dS ratio");</span>
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18
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<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
18
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC18" class="line" lang="plaintext"> </span>
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19
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19
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC19" class="line" lang="plaintext">bl_sum = 0;</span>
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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
20
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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
20
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC20" class="line" lang="plaintext">for (bl; in; (fitter.results["branch length"])["0"]){</span>
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