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<h3>
Benjamin Redelings pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/bali-phy">Debian Med / bali-phy</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bali-phy/commit/e73664112c1ff560964d8b60a4ba295719eebc05">e7366411</a></strong>
<div>
<span>by Benjamin Redelings</span>
<i>at 2018-06-13T18:42:12-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.1.5+dfsg</pre>
</li>
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<h4>26 changed files:</h4>
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<li class="file-stats">
<a href="#e26903080922fed937b6d35e65a8428fb2361d62">
doc/README.itex.xml
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<li class="file-stats">
<a href="#603935c0f5d92fa8814ce772faffafe38a068820">
<span class="new-file">
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doc/man/tree-tool.md
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<li class="file-stats">
<a href="#9a30e30f86d3b630c54165c6b3fc616577fdf300">
<span class="new-file">
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functions/Frequencies/uniform.json
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<li class="file-stats">
<a href="#6a077de4125eaeaf6c8e6fd042e50c25f1e3e9f6">
functions/Rates/free.json
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<li class="file-stats">
<a href="#05fe8ad203e9b9d4353037be294ed4b888d84be0">
functions/fMutSel.json
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<li class="file-stats">
<a href="#5c3b89e47dc707d952d986825a57fa39a5352afc">
functions/fMutSel0.json
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<li class="file-stats">
<a href="#1b06553ce684a58869b19b8d4d8e1ebd75fd7273">
functions/functions/dna.json
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<li class="file-stats">
<a href="#0cc1139e3347f573ae1feee5b73dbc8a8a21fcfa">
meson.build
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<li class="file-stats">
<a href="#507e3b07585af664592febc114bcde78fa897606">
modules/SModel.hs
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<li class="file-stats">
<a href="#084fd92134dca1a928080e561b8573277c2f7609">
scripts/bp-analyze
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<li class="file-stats">
<a href="#e0eb72319dafa1e48cc1ff017dd55138b7106de3">
src/alignment/alignment-constraint.H
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<li class="file-stats">
<a href="#c20d0a06cb220addaa5dc6796e09bb79ab929ba2">
src/bali-phy.cc
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<li class="file-stats">
<a href="#33e83749497034e5ac312f2678d52d0f6a7f7d55">
src/builtins/SModel.cc
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<li class="file-stats">
<a href="#4f47dd698d0f371017c7c869bc9e2e6216e62843">
src/computation/computation.cc
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<li class="file-stats">
<a href="#65b7ddf0e798fdf9c7be21320e917f152ca95966">
src/dp/dp-matrix.H
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<li class="file-stats">
<a href="#4478b68e32aa01051ad81e4f640ceda3a06b49c3">
src/dp/dp-matrix.cc
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<a href="#8361e1c55986c0d3f13504b2f7538e282eaf9893">
src/mcmc/sample-alignment.cc
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<li class="file-stats">
<a href="#17867de5076d50e87826675d7ed81840420e4676">
src/meson.build
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<li class="file-stats">
<a href="#2a12133bc14e512e4352b8e3f5e2ad8d57e9cedc">
src/models/parameters.cc
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<li class="file-stats">
<a href="#793e98e2860c5009cc477e9a83aeadbab0aa9081">
src/startup/A-T-model.H
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<li class="file-stats">
<a href="#d58858ee516bfdb1c86c6b43708b0bdc4329e15b">
src/startup/A-T-model.cc
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<li class="file-stats">
<a href="#d3080ca51f439f576222fc20bb9459e84cd0f607">
src/startup/help.cc
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<li class="file-stats">
<a href="#b08039b44d681fdea6e22ae2712d6e01307dad0a">
src/substitution/substitution.cc
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<li class="file-stats">
<a href="#66d5dbdd0848e5daf8dd55d33e87059e24b62551">
src/tools/alignment-draw.cc
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<li class="file-stats">
<a href="#c71ed633fd98d76cd79b35c4870d0093fbf370bd">
src/tools/alignments-diff.cc
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<li class="file-stats">
<a href="#84999b84377c68efe88974cfb9b4180e6d617841">
<span class="new-file">
+
src/tools/tree-tool.cc
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<h4>Changes:</h4>
<li id="e26903080922fed937b6d35e65a8428fb2361d62">
<a href="https://salsa.debian.org/med-team/bali-phy/commit/e73664112c1ff560964d8b60a4ba295719eebc05#e26903080922fed937b6d35e65a8428fb2361d62"><strong>doc/README.itex.xml</strong></a>
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1
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;"><!DOCTYPE book [</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;"><!ENTITY version "3.1" ></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;"><!ENTITY version "3.1<span class="idiff left right">.4</span>" ></span></span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="xml"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;"><!ENTITY source.file "bali-phy-&version;.tar.gz" ></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;"><!ENTITY linux64.file "bali-phy-&version;-linux64.tar.gz" ></span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -161,7 +161,8 @@ However, note that this might conflict with R installed from other places, such </td>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="xml"></span>
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<td class="diff-line-num old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="xml"> <span class="nt" style="color: navy;"><section><info><title></span>Install on Linux<span class="nt" style="color: navy;"></title></info></span></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="xml"></span>
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<td class="diff-line-num old old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="xml"> <span class="nt" style="color: navy;"><section><info><title></span>Install BAli-Phy using <span class="nt" style="color: navy;"><command></span>apt-get<span class="nt" style="color: navy;"></command></span> (recommended if using <span class="nt" style="color: navy;"><emphasis></span>Debian: testing or unstable<span class="nt" style="color: navy;"></emphasis></span>)<span class="nt" style="color: navy;"></title></info></span></span>
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<td class="diff-line-num new old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="xml"> <span class="nt" style="color: navy;"><section><info><title></span>Install BAli-Phy using <span class="nt" style="color: navy;"><command></span>apt-get<span class="nt" style="color: navy;"></command></title></info></span></span>
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<td class="diff-line-num new old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="xml"> BAli-Phy is available on Ubuntu <span class="nt" style="color: navy;"><link</span> <span class="na" style="color: teal;">xmlns:xlink=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xlink"</span> <span class="na" style="color: teal;">xlink:href=</span><span class="s" style="color: #d14;">"https://launchpad.net/ubuntu/+source/bali-phy/"</span><span class="nt" style="color: navy;">></span>("Cosmic Cuttlefish" or later)<span class="nt" style="color: navy;"></link></span>, and Debian (<span class="nt" style="color: navy;"><link</span> <span class="na" style="color: teal;">xmlns:xlink=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xlink"</span> <span class="na" style="color: teal;">xlink:href=</span><span class="s" style="color: #d14;">"https://packages.debian.org/search?keywords=bali-phy&searchon=names&section=all"</span><span class="nt" style="color: navy;">></span>testing and unstable<span class="nt" style="color: navy;"></link></span>).</span>
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<td class="diff-line-num new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="xml"> <span class="nt" style="color: navy;"><screen><prompt></span>%<span class="nt" style="color: navy;"></prompt></span> <span class="nt" style="color: navy;"><userinput></span>sudo apt-get install bali-phy<span class="nt" style="color: navy;"></userinput></screen></span></span>
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<td class="diff-line-num old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="xml"> Check that the executable runs:</span>
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<td class="diff-line-num old_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="xml"> <span class="nt" style="color: navy;"><screen><prompt></span>%<span class="nt" style="color: navy;"></prompt></span> <span class="nt" style="color: navy;"><userinput></span>bali-phy --version<span class="nt" style="color: navy;"></userinput></screen></span></span>
</pre>
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</li>
<li id="603935c0f5d92fa8814ce772faffafe38a068820">
<a href="https://salsa.debian.org/med-team/bali-phy/commit/e73664112c1ff560964d8b60a4ba295719eebc05#603935c0f5d92fa8814ce772faffafe38a068820"><strong>doc/man/tree-tool.md</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown">% tree-tool(1)</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown">% Benjamin Redelings</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown">% Feb 2018</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gh" style="color: #999;"># NAME</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**tree-tool**</span> -- Perform various operations on Newick trees.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="gh" style="color: #999;"># SYNOPSIS</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**tree-tool**</span> _tree-file_ <span class="p">[</span><span class="nv" style="color: teal;">OPTIONS</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="gh" style="color: #999;"># DESCRIPTION</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown">Perform various operations on Newick trees.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="gh" style="color: #999;"># GENERAL OPTIONS:</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**-h**</span>, <span class="gs" style="font-weight: 600;">**--help**</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown">: produce help message</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**-v**</span>, <span class="gs" style="font-weight: 600;">**--verbose**</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown">: Output more log messages on stderr.</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**--prune**</span> _arg_</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown">: Comma-separated taxa to remove</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**--resolve**</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown">: Comma-separated taxa to remove</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"><span class="gh" style="color: #999;"># REPORTING BUGS:</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"> BAli-Phy online help: <span class="nv" style="color: teal;"><http://www.bali-phy.org/docs.php></span>.</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown">Please send bug reports to <span class="nv" style="color: teal;"><bali-phy-users@googlegroups.com></span>.</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"></span></pre>
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<li id="9a30e30f86d3b630c54165c6b3fc616577fdf300">
<a href="https://salsa.debian.org/med-team/bali-phy/commit/e73664112c1ff560964d8b60a4ba295719eebc05#9a30e30f86d3b630c54165c6b3fc616577fdf300"><strong>functions/Frequencies/uniform.json</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="json"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Frequencies.uniform"</span><span class="p">,</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"result_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"List[Pair[String,Double]]"</span><span class="p">,</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"call"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"SModel.uniform_frequencies[a]"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"args"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"a"</span><span class="p">,</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"arg_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"a"</span><span class="p">,</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"getAlphabet"</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">}</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">],</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"examples"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;">"hky85[pi=Frequencies.uniform]"</span><span class="p">]</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="json"><span class="p">}</span></span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,5 +30,13 @@</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"title"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Free rates model"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"description"</span><span class="p">:</span><span class="s2" style="color: #d14;">"Rate heterogeneity model where the rate and frequency of each category can be estimated from the data."</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"examples"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;">"hky85+Rates.free[n=3]"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"examples"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;">"hky85+Rates.free[n=3]"</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"citation"</span><span class="p">:{</span><span class="s2" style="color: #d14;">"type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"article"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"title"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"A space-time process model for the evolution of DNA sequences."</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"year"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"1995"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"author"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[{</span><span class="s2" style="color: #d14;">"name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Yang, Ziheng"</span><span class="p">}],</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"journal"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span><span class="s2" style="color: #d14;">"name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Genetics"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"volume"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"139"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"number"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"2"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"pages"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"993--1005"</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"identifier"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[{</span><span class="s2" style="color: #d14;">"type"</span><span class="p">:</span><span class="s2" style="color: #d14;">"pmid"</span><span class="p">,</span><span class="s2" style="color: #d14;">"id"</span><span class="p">:</span><span class="s2" style="color: #d14;">"7713447"</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">{</span><span class="s2" style="color: #d14;">"type"</span><span class="p">:</span><span class="s2" style="color: #d14;">"pmcid"</span><span class="p">,</span><span class="s2" style="color: #d14;">"id"</span><span class="p">:</span><span class="s2" style="color: #d14;">"PMC1206396"</span><span class="p">}]</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="json"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/e73664112c1ff560964d8b60a4ba295719eebc05#05fe8ad203e9b9d4353037be294ed4b888d84be0"><strong>functions/fMutSel.json</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,24 +6,35 @@</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"omega"</span><span class="p">,</span></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"arg_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Double"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"~uniform[0,1]"</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"~uniform[0,1]"</span><span class="p">,</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Excess dN/dS"</span></span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"w"</span><span class="p">,</span></span>
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13
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"arg_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"List[Pair[String,Double]]"</span><span class="p">,</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"zip[letters[A],~iid[length[letters[A]],log_normal[0,0.5]]]"</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"zip[letters[A],~iid[length[letters[A]],log_normal[0,0.5]]]"</span><span class="p">,</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Fitness of codons"</span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"submodel"</span><span class="p">,</span></span>
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18
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"arg_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"RevCTMC[a]"</span><span class="p">,</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"hky85_sym"</span><span class="p">,</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"alphabet"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"getNucleotides[A]"</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"hky85"</span><span class="p">,</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"alphabet"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"getNucleotides[A]"</span><span class="p">,</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Model of neutral nucleotide substitution"</span></span>
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21
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"A"</span><span class="p">,</span></span>
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24
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"arg_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Codons[a]"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"getAlphabet"</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"getAlphabet"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"The alphabet"</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">}</span></span>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"extract"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"all"</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"extract"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"all"</span><span class="p">,</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"citation"</span><span class="p">:{</span><span class="s2" style="color: #d14;">"type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"article"</span><span class="p">,</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"title"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage"</span><span class="p">,</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"year"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"2008"</span><span class="p">,</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"author"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[{</span><span class="s2" style="color: #d14;">"name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Yang, Ziheng"</span><span class="p">},{</span><span class="s2" style="color: #d14;">"name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Nielsen, Rasmus"</span><span class="p">}],</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"journal"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span><span class="s2" style="color: #d14;">"name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Molecular Biology and Evolution"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"volume"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"25"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"number"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"3"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"pages"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"568--579"</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"identifier"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[{</span><span class="s2" style="color: #d14;">"type"</span><span class="p">:</span><span class="s2" style="color: #d14;">"doi"</span><span class="p">,</span><span class="s2" style="color: #d14;">"id"</span><span class="p">:</span><span class="s2" style="color: #d14;">"10.1093/molbev/msm284"</span><span class="p">}]</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="json"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/e73664112c1ff560964d8b60a4ba295719eebc05#5c3b89e47dc707d952d986825a57fa39a5352afc"><strong>functions/fMutSel0.json</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,24 +6,35 @@</td>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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7
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"omega"</span><span class="p">,</span></span>
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8
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"arg_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Double"</span><span class="p">,</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"~uniform[0,1]"</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"~uniform[0,1]"</span><span class="p">,</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Excess dN/dS"</span></span>
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10
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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11
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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12
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"w"</span><span class="p">,</span></span>
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13
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"arg_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"List[Pair[String,Double]]"</span><span class="p">,</span></span>
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14
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<td class="diff-line-num new_line old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"zip[letters[getAminoAcids[A]],~iid[length[letters[getAminoAcids[A]]],log_normal[0,0.5]]]"</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"zip[letters[getAminoAcids[A]],~iid[length[letters[getAminoAcids[A]]],log_normal[0,0.5]]]"</span><span class="p">,</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Fitness of amino acids"</span></span>
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15
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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16
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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17
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"submodel"</span><span class="p">,</span></span>
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18
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"arg_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"RevCTMC[a]"</span><span class="p">,</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"hky85_sym"</span><span class="p">,</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"alphabet"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"getNucleotides[A]"</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"hky85"</span><span class="p">,</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"alphabet"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"getNucleotides[A]"</span><span class="p">,</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Model of neutral nucleotide substitution"</span></span>
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21
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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22
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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23
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"A"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"arg_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Codons[a]"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"getAlphabet"</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"getAlphabet"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"The alphabet"</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"extract"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"all"</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"extract"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"all"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"citation"</span><span class="p">:{</span><span class="s2" style="color: #d14;">"type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"article"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"title"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"year"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"2008"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"author"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[{</span><span class="s2" style="color: #d14;">"name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Yang, Ziheng"</span><span class="p">},{</span><span class="s2" style="color: #d14;">"name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Nielsen, Rasmus"</span><span class="p">}],</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"journal"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span><span class="s2" style="color: #d14;">"name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Molecular Biology and Evolution"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"volume"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"25"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"number"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"3"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"pages"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"568--579"</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"identifier"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[{</span><span class="s2" style="color: #d14;">"type"</span><span class="p">:</span><span class="s2" style="color: #d14;">"doi"</span><span class="p">,</span><span class="s2" style="color: #d14;">"id"</span><span class="p">:</span><span class="s2" style="color: #d14;">"10.1093/molbev/msm284"</span><span class="p">}]</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="json"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/e73664112c1ff560964d8b60a4ba295719eebc05#1b06553ce684a58869b19b8d4d8e1ebd75fd7273"><strong>functions/functions/dna.json</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="json"><span class="p">{</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"dna"</span><span class="p">,</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"synonyms"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="w" style="color: #bbb;"><span class="idiff left"> </span></span><span class="s2" style="color: #d14;"><span class="idiff">"DNA"</span></span><span class="w" style="color: #bbb;"><span class="idiff right"> </span></span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"synonyms"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;"><span class="idiff left right">"DNA"</span></span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"result_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"DNA"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"call"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Alphabet.dna"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"args"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[],</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"title"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"The <span class="idiff left right">R</span>NA alphabet"</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"title"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"The <span class="idiff left right">D</span>NA alphabet"</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="json"><span class="p">}</span></span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">project('bali-phy', ['cpp','c'],</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> version: '3.1.<span class="idiff left right">4</span>',</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> version: '3.1.<span class="idiff left right">5</span>',</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> default_options : [</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> 'buildtype=release',</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> 'cpp_std=c++14'</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,7 +37,7 @@ builtin calc_root_probability 7 "calc_root_probability" "SModel";</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="haskell"><span class="n" style="color: #333;">builtin</span> <span class="n" style="color: #333;">bitmask_from_alignment</span> <span class="mi" style="color: #099;">2</span> <span class="s" style="color: #d14;">"bitmask_from_alignment"</span> <span class="s" style="color: #d14;">"Alignment"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="haskell"><span class="n" style="color: #333;">builtin</span> <span class="n" style="color: #333;">peel_leaf_branch_SEV</span> <span class="mi" style="color: #099;">4</span> <span class="s" style="color: #d14;">"peel_leaf_branch_SEV"</span> <span class="s" style="color: #d14;">"SModel"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="haskell"><span class="n" style="color: #333;">builtin</span> <span class="n" style="color: #333;">peel_internal_branch_SEV</span> <span class="mi" style="color: #099;">4</span> <span class="s" style="color: #d14;">"peel_internal_branch_SEV"</span> <span class="s" style="color: #d14;">"SModel"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="haskell"><span class="n" style="color: #333;">builtin</span> <span class="n" style="color: #333;">calc_root_probability_SEV</span> <span class="mi" style="color: #099;"><span class="idiff left right">4</span></span> <span class="s" style="color: #d14;">"calc_root_probability_SEV"</span> <span class="s" style="color: #d14;">"SModel"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="haskell"><span class="n" style="color: #333;">builtin</span> <span class="n" style="color: #333;">calc_root_probability_SEV</span> <span class="mi" style="color: #099;"><span class="idiff left right">5</span></span> <span class="s" style="color: #d14;">"calc_root_probability_SEV"</span> <span class="s" style="color: #d14;">"SModel"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="haskell"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="haskell"><span class="n" style="color: #333;">builtin</span> <span class="n" style="color: #333;">peel_likelihood_1</span> <span class="mi" style="color: #099;">3</span> <span class="s" style="color: #d14;">"peel_likelihood_1"</span> <span class="s" style="color: #d14;">"SModel"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="haskell"><span class="n" style="color: #333;">builtin</span> <span class="n" style="color: #333;">peel_likelihood_2</span> <span class="mi" style="color: #099;">6</span> <span class="s" style="color: #d14;">"peel_likelihood_2"</span> <span class="s" style="color: #d14;">"SModel"</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -130,6 +130,9 @@ frequency_matrix (MixtureModel d) = let {model = MixtureModel d}</td>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="haskell"><span class="n" style="color: #333;">frequency_matrix</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">MixtureModels</span> <span class="p">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">ms</span><span class="p">))</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">frequency_matrix</span> <span class="n" style="color: #333;">m</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="haskell"></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="haskell"><span class="c1" style="color: #998; font-style: italic;">--</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="haskell"><span class="n" style="color: #333;">uniform_frequencies</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">zip</span> <span class="n" style="color: #333;">letters</span> <span class="p">(</span><span class="n" style="color: #333;">repeat</span> <span class="o" style="font-weight: 600;">$</span> <span class="mf" style="color: #099;">1.0</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">intToDouble</span> <span class="n" style="color: #333;">n_letters</span><span class="p">))</span> <span class="kr" style="font-weight: 600;">where</span> <span class="p">{</span><span class="n" style="color: #333;">letters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alphabet_letters</span> <span class="n" style="color: #333;">a</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="haskell"> <span class="n" style="color: #333;">n_letters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alphabetSize</span> <span class="n" style="color: #333;">a</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="haskell"></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="haskell"><span class="n" style="color: #333;">plus_f_equal_frequencies</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">plus_f</span> <span class="n" style="color: #333;">a</span> <span class="p">(</span><span class="n" style="color: #333;">replicate</span> <span class="n" style="color: #333;">n_letters</span> <span class="p">(</span><span class="mf" style="color: #099;">1.0</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">intToDouble</span> <span class="n" style="color: #333;">n_letters</span><span class="p">))</span> <span class="kr" style="font-weight: 600;">where</span> <span class="p">{</span><span class="n" style="color: #333;">n_letters</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">alphabetSize</span> <span class="n" style="color: #333;">a</span><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="haskell"></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="haskell"><span class="n" style="color: #333;">jukes_cantor</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reversible_markov</span> <span class="p">(</span><span class="n" style="color: #333;">equ</span> <span class="n" style="color: #333;">a</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">plus_f_equal_frequencies</span> <span class="n" style="color: #333;">a</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -227,13 +230,6 @@ get_element_freqs ((key,value):rest) x = if (key == x) then value else get_eleme</td>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="haskell"><span class="n" style="color: #333;">get_element_exchange</span> <span class="kt" style="color: #458; font-weight: 600;">[]</span> <span class="n" style="color: #333;">x</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">error</span> <span class="p">(</span><span class="s" style="color: #d14;">"No exchangeability specified for '"</span> <span class="o" style="font-weight: 600;">++</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">++</span> <span class="s" style="color: #d14;">"'"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="haskell"><span class="n" style="color: #333;">get_element_exchange</span> <span class="p">((</span><span class="n" style="color: #333;">key</span><span class="p">,</span><span class="n" style="color: #333;">value</span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">rest</span><span class="p">)</span> <span class="n" style="color: #333;">x</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">y</span> <span class="kr" style="font-weight: 600;">then</span> <span class="n" style="color: #333;">value</span> <span class="kr" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">get_element_exchange</span> <span class="n" style="color: #333;">rest</span> <span class="n" style="color: #333;">x</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="haskell"></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="haskell"><span class="n" style="color: #333;">constant_frequencies_model</span> <span class="n" style="color: #333;">freqs</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span> <span class="p">[</span><span class="n" style="color: #333;">get_element_freqs</span> <span class="n" style="color: #333;">freqs</span> <span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">|</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">alphabet_letters</span> <span class="n" style="color: #333;">a</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="haskell"></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="haskell"><span class="n" style="color: #333;">perform_hash</span> <span class="kt" style="color: #458; font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">return</span> <span class="kt" style="color: #458; font-weight: 600;">[]</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="haskell"><span class="n" style="color: #333;">perform_hash</span> <span class="p">((</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">y</span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">xys</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">do</span> <span class="p">{</span><span class="n" style="color: #333;">y'</span> <span class="o" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">y</span><span class="p">;</span> <span class="n" style="color: #333;">xys'</span> <span class="o" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">perform_hash</span> <span class="n" style="color: #333;">xys</span><span class="p">;</span> <span class="n" style="color: #333;">return</span> <span class="p">((</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">y'</span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">xys'</span><span class="p">)};</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="haskell"></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="haskell"><span class="n" style="color: #333;">constant_frequencies_model2</span> <span class="n" style="color: #333;">freqs</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">do</span> <span class="p">{</span><span class="n" style="color: #333;">freqs'</span> <span class="o" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">freqs</span><span class="p">;</span> <span class="n" style="color: #333;">return</span> <span class="p">[</span><span class="n" style="color: #333;">get_element_freqs</span> <span class="n" style="color: #333;">freqs'</span> <span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">|</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">alphabet_letters</span> <span class="n" style="color: #333;">a</span><span class="p">]};</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="haskell"></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="haskell"><span class="n" style="color: #333;">select_element</span> <span class="n" style="color: #333;">x</span> <span class="p">((</span><span class="n" style="color: #333;">key</span><span class="p">,</span><span class="n" style="color: #333;">value</span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">rest</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">key</span> <span class="kr" style="font-weight: 600;">then</span> <span class="n" style="color: #333;">value</span> <span class="kr" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">select_element</span> <span class="n" style="color: #333;">x</span> <span class="n" style="color: #333;">rest</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="haskell"><span class="n" style="color: #333;">select_element</span> <span class="n" style="color: #333;">x</span> <span class="kt" style="color: #458; font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">error</span> <span class="o" style="font-weight: 600;">$</span> <span class="s" style="color: #d14;">"Can't find element "</span> <span class="o" style="font-weight: 600;">++</span> <span class="n" style="color: #333;">show</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">++</span> <span class="s" style="color: #d14;">" in dictionary!"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="haskell"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -386,6 +382,6 @@ cached_conditional_likelihoods_SEV t seqs alpha ps f a =</td>
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="haskell"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="haskell"> <span class="kr" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lc</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="haskell"></span>
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="haskell"><span class="n" style="color: #333;">peel_likelihood_SEV</span> <span class="n" style="color: #333;">t</span> <span class="n" style="color: #333;">cl</span> <span class="n" style="color: #333;">f</span> <span class="n" style="color: #333;">root</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">let</span> <span class="p">{</span><span class="n" style="color: #333;">branches_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">map</span> <span class="p">(</span><span class="n" style="color: #333;">reverseEdge</span> <span class="n" style="color: #333;">t</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">edgesOutOfNode</span> <span class="n" style="color: #333;">t</span> <span class="n" style="color: #333;">root</span><span class="p">);}</span> <span class="kr" style="font-weight: 600;">in</span></span>
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="haskell"> <span class="kr" style="font-weight: 600;"><span class="idiff left">case</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">branches_in</span></span><span class="idiff"> </span><span class="kr" style="font-weight: 600;"><span class="idiff">of</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{[</span></span><span class="n" style="color: #333;"><span class="idiff">b1</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">b2</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">b3</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">calc_root_probability_SEV</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">cl</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">b1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">cl</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">b2</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">cl</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">b3</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">f</span></span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="haskell"><span class="n" style="color: #333;">peel_likelihood_SEV</span> <span class="n" style="color: #333;">t</span> <span class="n" style="color: #333;">cl</span> <span class="n" style="color: #333;">f</span> <span class="n" style="color: #333;">root</span> <span class="n" style="color: #333;"><span class="idiff left">counts</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">let</span> <span class="p">{</span><span class="n" style="color: #333;">branches_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">map</span> <span class="p">(</span><span class="n" style="color: #333;">reverseEdge</span> <span class="n" style="color: #333;">t</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">edgesOutOfNode</span> <span class="n" style="color: #333;">t</span> <span class="n" style="color: #333;">root</span><span class="p">);}</span> <span class="kr" style="font-weight: 600;">in</span></span>
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="haskell"> <span class="idiff left"> </span><span class="kr" style="font-weight: 600;"><span class="idiff">case</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">branches_in</span></span><span class="idiff"> </span><span class="kr" style="font-weight: 600;"><span class="idiff">of</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{[</span></span><span class="n" style="color: #333;"><span class="idiff">b1</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">b2</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">b3</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">calc_root_probability_SEV</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">cl</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">b1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">cl</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">b2</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">cl</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">b3</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">counts</span></span><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="haskell"><span class="p">}</span></span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -126,6 +126,7 @@ for(my $i=1;$i<=$#commands;$i++)</td>
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126
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="html"> <span class="na" style="color: teal;">print</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: teal;">WARNING:</span> <span class="na" style="color: teal;">Commands</span> <span class="na" style="color: teal;">differ</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">!\</span><span class="na" style="color: teal;">n</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">commands</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="na" style="color: teal;">0</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">]\</span><span class="na" style="color: teal;">n</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">commands</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[$</span><span class="na" style="color: teal;">i</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">]\</span><span class="na" style="color: teal;">n</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">";</span></span>
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127
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="html"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">}</span></span>
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128
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="html"><span class="err" style="color: #a61717; background-color: #e3d2d2;">}</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="html"></span>
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129
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="html"><span class="err" style="color: #a61717; background-color: #e3d2d2;">@</span><span class="na" style="color: teal;">directories =</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"> </span><span class="s" style="color: #d14;">get_header_attributes("directory",@out_files);</span></span>
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130
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="html"><span class="na" style="color: teal;">my</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">directories_differ=</span><span class="s" style="color: #d14;">0;</span></span>
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131
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<td class="diff-line-num new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="html"><span class="na" style="color: teal;">for</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">my</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">i=</span><span class="s" style="color: #d14;">1;$i<=$#directories;$i++)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -133,6 +134,13 @@ for(my $i=1;$i<=$#directories;$i++)</td>
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133
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<td class="diff-line-num new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="html"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">directories_differ=</span><span class="s" style="color: #d14;">1</span> <span class="na" style="color: teal;">if</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">($</span><span class="na" style="color: teal;">directories</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[$</span><span class="na" style="color: teal;">i</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span> <span class="na" style="color: teal;">ne</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">directories</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="na" style="color: teal;">0</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">]);</span></span>
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134
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="html"><span class="err" style="color: #a61717; background-color: #e3d2d2;">}</span></span>
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135
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="html"></span>
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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="html"><span class="na" style="color: teal;">my</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@</span><span class="na" style="color: teal;">versions =</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"> </span><span class="s" style="color: #d14;">get_all_versions();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="html"><span class="na" style="color: teal;">my</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">versions_differ=</span><span class="s" style="color: #d14;">0;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="html"><span class="na" style="color: teal;">for</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">my</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">i=</span><span class="s" style="color: #d14;">1;$i<=$#versions;$i++)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="html"><span class="err" style="color: #a61717; background-color: #e3d2d2;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="html"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">versions_differ=</span><span class="s" style="color: #d14;">1</span> <span class="na" style="color: teal;">if</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">($</span><span class="na" style="color: teal;">versions</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[$</span><span class="na" style="color: teal;">i</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span> <span class="na" style="color: teal;">ne</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">versions</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="na" style="color: teal;">0</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">]);</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="html"><span class="err" style="color: #a61717; background-color: #e3d2d2;">}</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="html"></span>
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136
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<td class="diff-line-num new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="html"><span class="err" style="color: #a61717; background-color: #e3d2d2;">@</span><span class="na" style="color: teal;">subdirs =</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"> </span><span class="s" style="color: #d14;">get_header_attributes("subdirectory",@out_files);</span></span>
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137
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="html"></span>
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138
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<td class="diff-line-num new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="html"><span class="na" style="color: teal;">my</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">betas =</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"> </span><span class="s" style="color: #d14;">get_cmdline_attribute("beta");</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -384,8 +392,8 @@ sub html_header</td>
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<td class="diff-line-num old_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
384
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<td class="diff-line-num new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="html"></span>
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<td class="diff-line-num old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
385
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<td class="diff-line-num new_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="html"> <span class="nt" style="color: navy;">th</span> <span class="p">{</span><span class="nl">padding-left</span><span class="p">:</span> <span class="m" style="color: #099;">0.5em</span><span class="p">;</span> <span class="nl">padding-right</span><span class="p">:</span><span class="m" style="color: #099;">0.5em</span><span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
386
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<td class="diff-line-num new_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="html"> <span class="nt" style="color: navy;">td</span> <span class="p">{</span><span class="nl">padding</span><span class="p">:</span> <span class="m" style="color: #099;">0.1em</span><span class="p">;}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
387
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<td class="diff-line-num new_line old" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="html"> <span class="nt" style="color: navy;"><span class="idiff left">td</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="nl"><span class="idiff">padding-left</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff right">0.3</span>em</span><span class="p">;}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
388
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<td class="diff-line-num new_line old" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="html"> <span class="nt" style="color: navy;"><span class="idiff left">td</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="nl"><span class="idiff">padding-right</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff right">0.3</span>em</span><span class="p">;}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="html"> <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left">.backlit2</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">td</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="nl"><span class="idiff">padding-left</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff right">0.5</span>em</span><span class="p">;}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="html"> <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left">.backlit2</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">td</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="nl"><span class="idiff">padding-right</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff right">1.0</span>em</span><span class="p">;}</span></span>
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<td class="diff-line-num old_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
389
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<td class="diff-line-num new_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="html"></span>
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<td class="diff-line-num old_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
390
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<td class="diff-line-num new_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="html"><span class="nf" style="color: #900; font-weight: 600;">#topbar</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
391
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<td class="diff-line-num new_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
399
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC399" class="line" lang="html"> <span class="nl">background-color</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">rgb</span><span class="p">(</span><span class="m" style="color: #099;">201</span><span class="p">,</span><span class="m" style="color: #099;">217</span><span class="p">,</span><span class="m" style="color: #099;">233</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -393,6 +401,8 @@ sub html_header</td>
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<td class="diff-line-num old_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
393
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<td class="diff-line-num new_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="html"> <span class="nl">padding</span><span class="p">:</span> <span class="m" style="color: #099;">0.5em</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
394
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<td class="diff-line-num new_line" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="html"> <span class="nl">display</span><span class="p">:</span> <span class="n" style="color: #333;">table</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
395
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<td class="diff-line-num new_line" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="html"> <span class="nl">width</span><span class="p">:</span> <span class="m" style="color: #099;">100%</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="html"> <span class="nl">position</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">fixed</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="html"> <span class="nl">top</span><span class="p">:</span> <span class="m" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
396
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<td class="diff-line-num new_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="html"><span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
397
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<td class="diff-line-num new_line" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="html"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
398
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<td class="diff-line-num new_line" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="html"><span class="nf" style="color: #900; font-weight: 600;">#topbar</span> <span class="nf" style="color: #900; font-weight: 600;">#menu</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -407,11 +417,12 @@ sub html_header</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
407
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<td class="diff-line-num new_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
417
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC417" class="line" lang="html"> <span class="nl">white-space</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">nowrap</span><span class="p">;</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="html"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="html"> <span class="nc" style="color: #458; font-weight: 600;">.content</span> <span class="p">{</span><span class="nl">margin</span><span class="p">:</span><span class="m" style="color: #099;">1em</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="html"> <span class="nc" style="color: #458; font-weight: 600;">.content</span> <span class="p">{</span><span class="nl">margin</span><span class="p">:</span><span class="m" style="color: #099;">1em</span><span class="p"><span class="idiff left">;</span></span><span class="idiff"> </span><span class="nl"><span class="idiff">margin-top</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff right">3em</span></span><span class="p">}</span></span>
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411
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="html"> <span class="nc" style="color: #458; font-weight: 600;">.backlit</span> <span class="nt" style="color: navy;">td</span> <span class="p">{</span><span class="nl">background</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">rgb</span><span class="p">(</span><span class="m" style="color: #099;">220</span><span class="p">,</span><span class="m" style="color: #099;">220</span><span class="p">,</span><span class="m" style="color: #099;">220</span><span class="p">);}</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="html"> <span class="nc" style="color: #458; font-weight: 600;">.anchor</span> <span class="p">{</span><span class="nl">position</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">relative</span><span class="p">;</span> <span class="nl">top</span><span class="p">:</span> <span class="m" style="color: #099;">-3em</span><span class="p">}</span></span>
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412
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423
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="html"></span>
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413
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424
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="html"> <span class="nt" style="color: navy;">h1</span> <span class="p">{</span><span class="nl">font-size</span><span class="p">:</span> <span class="m" style="color: #099;">150%</span><span class="p">;}</span></span>
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414
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="html"> <span class="nt" style="color: navy;">h2</span> <span class="p">{</span><span class="nl">font-size</span><span class="p">:</span> <span class="m" style="color: #099;">130%</span><span class="p">;</span> <span class="nl">margin-top</span><span class="p">:</span><span class="m" style="color: #099;">2<span class="idiff left">em</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="nl"><span class="idiff">margin-bottom</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff right">0.2</span>em</span><span class="p">}</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="html"> <span class="nt" style="color: navy;">h2</span> <span class="p">{</span><span class="nl">font-size</span><span class="p">:</span> <span class="m" style="color: #099;">130%</span><span class="p">;</span> <span class="nl">margin-top</span><span class="p">:</span><span class="m" style="color: #099;">2<span class="idiff left">.5em</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="nl"><span class="idiff">margin-bottom</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff right">1</span>em</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="html"> <span class="nt" style="color: navy;">h3</span> <span class="p">{</span><span class="nl">font-size</span><span class="p">:</span> <span class="m" style="color: #099;">110%</span><span class="p">;</span> <span class="nl">margin-bottom</span><span class="p">:</span> <span class="m" style="color: #099;">0.2em</span><span class="p">}</span><span class="o" style="font-weight: 600;">//</span> <span class="nt" style="color: navy;">margin-top</span><span class="o" style="font-weight: 600;">:</span> <span class="nt" style="color: navy;">0</span><span class="nc" style="color: #458; font-weight: 600;">.3em</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">}</span></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="html"> <span class="nt" style="color: navy;">ul</span> <span class="p">{</span><span class="nl">margin-top</span><span class="p">:</span> <span class="m" style="color: #099;">0.4em</span><span class="p">;}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -445,8 +456,8 @@ sub topbar</td>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="html"> <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"menu"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="html"> [<span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#data"</span><span class="nt" style="color: navy;">></span>Data+Model<span class="nt" style="color: navy;"></a></span>]</span>
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="html"> [<span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#parameters"</span><span class="nt" style="color: navy;">></span>Parameters<span class="nt" style="color: navy;"></a></span>]</span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="html"> [<span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#alignment"</span><span class="nt" style="color: navy;">></span>Alignment<span class="nt" style="color: navy;"></a></span>]</span>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="html"> [<span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#topology"</span><span class="nt" style="color: navy;">></span>Phylogeny<span class="nt" style="color: navy;"></a></span>]</span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="html"> [<span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#alignment"</span><span class="nt" style="color: navy;">></span>Alignment<span class="nt" style="color: navy;"></a></span>]</span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="html"> [<span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#mixing"</span><span class="nt" style="color: navy;">></span>Mixing<span class="nt" style="color: navy;"></a></span>]</span>
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451
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462
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="html"> [<span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#analysis"</span><span class="nt" style="color: navy;">></span>Analysis<span class="nt" style="color: navy;"></a></span>]</span>
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452
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463
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="html"> [<span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#models"</span><span class="nt" style="color: navy;">></span>Models+Priors<span class="nt" style="color: navy;"></a></span>]</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -496,7 +507,7 @@ sub print_models</td>
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496
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507
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="html"> {</span>
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497
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508
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="html"> my $model_name = $name.$i;</span>
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498
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509
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="html"> my ($assign, $model_html) = print_model($model);</span>
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499
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><tr><td><a</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">\"$model_name\"</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">\"<span class="idiff left">modelname\"</span></span><span class="nt" style="color: navy;"><span class="idiff">></span></span><span class="idiff">$model_name</span><span class="nt" style="color: navy;"><span class="idiff right"></a</span>></td><td></span>$assign<span class="nt" style="color: navy;"></td><td></span>\n";</span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><tr><td><a</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">\"$model_name\"</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">\"<span class="idiff left">anchor\"</span></span><span class="nt" style="color: navy;"><span class="idiff">></a><span</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"modelname\"</span></span><span class="nt" style="color: navy;"><span class="idiff">></span></span><span class="idiff">$model_name</span><span class="nt" style="color: navy;"><span class="idiff right"></span</span>></td><td></span>$assign<span class="nt" style="color: navy;"></td><td></span>\n";</span>
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500
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511
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="html"> $section .= $model_html;</span>
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501
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512
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"></td></tr></span>\n";</span>
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502
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513
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="html"> $i = $i + 1;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -509,7 +520,7 @@ sub print_models</td>
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509
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520
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="html">sub print_data_and_model</span>
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510
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521
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="html">{</span>
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511
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522
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="html"> my $section = "";</span>
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512
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">\"clear:both\"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;"><span class="idiff left">name=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"data\"</span></span><span class="nt" style="color: navy;"><span class="idiff">></span></span><span class="idiff">Data </span><span class="ni" style="color: purple;"><span class="idiff">&</span></span><span class="idiff"> Model</span><span class="nt" style="color: navy;"><span class="idiff right"></a></span></h2></span>\n";</span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">\"clear:both\"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;"><span class="idiff left">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"anchor\"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">name=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"data\"</span></span><span class="nt" style="color: navy;"><span class="idiff">></a></span></span><span class="idiff">Data </span><span class="ni" style="color: purple;"><span class="idiff">&</span></span><span class="idiff right"> Model</span><span class="nt" style="color: navy;"></h2></span>\n";</span>
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513
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524
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><table</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">\"backlit2\"</span><span class="nt" style="color: navy;">></span>\n";</span>
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514
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525
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><tr><th></span>Partition<span class="nt" style="color: navy;"></th><th></span>Sequences<span class="nt" style="color: navy;"></th><th></span>Lengths<span class="nt" style="color: navy;"></th><th></span>Alphabet<span class="nt" style="color: navy;"></th><th></span>Substitution<span class="ni" style="color: purple;"> </span>Model<span class="nt" style="color: navy;"></th><th></span>Indel<span class="ni" style="color: purple;"> </span>Model<span class="nt" style="color: navy;"></th><th></span>Scale<span class="ni" style="color: purple;"> </span>Model<span class="nt" style="color: navy;"></th></tr></span>\n";</span>
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<td class="diff-line-num old_line" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
515
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526
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="html"> for(my $p=0;$p<span class="nt" style="color: navy;"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">=$#</span><span class="na" style="color: teal;">input_file_names</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">;$</span><span class="na" style="color: teal;">p</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">++)</span> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -592,22 +603,22 @@ sub print_data_and_model</td>
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592
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603
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<pre style="margin: 0;"> <span id="LC603" class="line" lang="html">sub print_model_section</span>
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593
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604
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<pre style="margin: 0;"> <span id="LC604" class="line" lang="html">{</span>
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594
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605
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="html"></span>
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<td class="diff-line-num old old_line" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
595
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<pre style="margin: 0;">-<span id="LC595" class="line" lang="html"> my $section = "<span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">\"clear:both\"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;"><span class="idiff left">name=</span></span><span class="s" style="color: #d14;"><span class="idiff right">\"models\"</span></span><span class="nt" style="color: navy;">></span>Model and priors<span class="nt" style="color: navy;"></h2></span>\n";</span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="html"> my $section = "<span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">\"clear:both\"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;"><span class="idiff left">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"anchor\"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">name=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"models\"</span></span><span class="nt" style="color: navy;"><span class="idiff right">></a</span>></span>Model and priors<span class="nt" style="color: navy;"></h2></span>\n";</span>
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<td class="diff-line-num old_line" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
596
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607
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<pre style="margin: 0;"> <span id="LC607" class="line" lang="html"> </span>
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597
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<td class="diff-line-num new_line old" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC597" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><h3</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">\"clear:both\"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;"><span class="idiff left">name=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"tree\"</span></span><span class="nt" style="color: navy;"><span class="idiff">></span></span><span class="idiff">Tree (+priors)</span><span class="nt" style="color: navy;"><span class="idiff right"></a></span></h3></span>\n";</span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><h3</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">\"clear:both\"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;"><span class="idiff left">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"anchor\"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">name=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"tree\"</span></span><span class="nt" style="color: navy;"><span class="idiff">></a></span></span><span class="idiff right">Tree (+priors)</span><span class="nt" style="color: navy;"></h3></span>\n";</span>
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598
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<td class="diff-line-num new_line" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
609
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="html"># $section .= "<span class="nt" style="color: navy;"><table</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">\"backlit2\"</span><span class="nt" style="color: navy;">></span>\n";</span>
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599
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610
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><table></span>\n";</span>
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600
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<td class="diff-line-num new_line" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
611
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">\"modelname\"</span><span class="nt" style="color: navy;">></span>topology<span class="nt" style="color: navy;"></td><td></span>$topology_prior<span class="nt" style="color: navy;"></td></tr></span>" if (defined($topology_prior));</span>
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601
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612
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<pre style="margin: 0;"> <span id="LC612" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">\"modelname\"</span><span class="nt" style="color: navy;">></span>branch lengths<span class="nt" style="color: navy;"></td><td></span>$branch_prior<span class="nt" style="color: navy;"></td></tr></span>" if (defined($branch_prior));</span>
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602
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613
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"></table></span>\n";</span>
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603
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614
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="html"> </span>
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604
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<td class="diff-line-num new_line old" data-linenumber="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><h3</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">\"clear:both\"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;"><span class="idiff left">name=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"smodel\"</span></span><span class="nt" style="color: navy;"><span class="idiff">></span></span><span class="idiff">Substitution model (+priors) </span><span class="nt" style="color: navy;"><span class="idiff right"></a></span></h3></span>\n";</span>
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<td class="diff-line-num new new_line" data-linenumber="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><h3</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">\"clear:both\"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;"><span class="idiff left">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"anchor\"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">name=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"smodel\"</span></span><span class="nt" style="color: navy;"><span class="idiff">></a></span></span><span class="idiff right">Substitution model (+priors)</span><span class="nt" style="color: navy;"></h3></span>\n";</span>
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605
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616
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<pre style="margin: 0;"> <span id="LC616" class="line" lang="html"> $section .= print_models("S",\@smodels);</span>
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606
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617
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<pre style="margin: 0;"> <span id="LC617" class="line" lang="html"></span>
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<td class="diff-line-num old old_line" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
607
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<td class="diff-line-num new_line old" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC607" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><h3</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">\"clear:both\"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;"><span class="idiff left">name=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"imodel\"</span></span><span class="nt" style="color: navy;"><span class="idiff">></span></span><span class="idiff">Indel model (+priors)</span><span class="nt" style="color: navy;"><span class="idiff right"></a></span></h3></span>\n";</span>
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<td class="diff-line-num new old_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><h3</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">\"clear:both\"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;"><span class="idiff left">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"anchor\"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">name=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"imodel\"</span></span><span class="nt" style="color: navy;"><span class="idiff">></a></span></span><span class="idiff right">Indel model (+priors)</span><span class="nt" style="color: navy;"></h3></span>\n";</span>
</pre>
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608
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619
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<pre style="margin: 0;"> <span id="LC619" class="line" lang="html"> $section .= print_models("I",\@imodels);</span>
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609
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620
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="html"></span>
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<td class="diff-line-num old old_line" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
610
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<pre style="margin: 0;">-<span id="LC610" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><h3</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">\"clear:both\"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;"><span class="idiff left">name=</span></span><span class="s" style="color: #d14;"><span class="idiff right">\"scales\"</span></span><span class="nt" style="color: navy;">></span>Scales (+priors)<span class="nt" style="color: navy;"></h3></span>\n";</span>
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<td class="diff-line-num new old_line" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><h3</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">\"clear:both\"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;"><span class="idiff left">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"anchor\"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">name=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"scales\"</span></span><span class="nt" style="color: navy;"><span class="idiff right">></a</span>></span>Scales (+priors)<span class="nt" style="color: navy;"></h3></span>\n";</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
611
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622
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="html"> $section .= print_models("scale",\@scale_models);</span>
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612
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623
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="html"></span>
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<td class="diff-line-num old_line" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
613
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624
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="html"> return $section;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -617,14 +628,19 @@ sub section_analysis</td>
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617
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628
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="html">{</span>
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618
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<td class="diff-line-num new_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
629
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="html"> my $section = "";</span>
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<td class="diff-line-num old_line" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
619
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<td class="diff-line-num new_line" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
630
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><br/><hr/><br/></span>\n";</span>
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<td class="diff-line-num old old_line" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
620
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<td class="diff-line-num new_line old" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC620" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><h2><a</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">\"analysis\"</span><span class="nt" style="color: navy;">></span>Analysis<span class="nt" style="color: navy;"></a></h2></span>\n";</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
621
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<td class="diff-line-num new_line old" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC621" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><p</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">\"margin-bottom:0\"</span><span class="nt" style="color: navy;">><b></span>command line<span class="nt" style="color: navy;"></b></span>: $commands[0]<span class="nt" style="color: navy;"></p></span>\n" if (!$commands_differ);</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
622
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<td class="diff-line-num new_line old" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC622" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><p</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">\"margin-top:0\"</span><span class="nt" style="color: navy;">><b></span>directory<span class="nt" style="color: navy;"></b></span>: $directories[0]<span class="nt" style="color: navy;"></p></span>\n" if (!$directories_differ);</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><h2><a</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">\"anchor\"</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">\"analysis\"</span><span class="nt" style="color: navy;">></a></span>Analysis<span class="nt" style="color: navy;"></h2></span>\n";</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><p></span>" if (!$commands_differ || !$directories_differ || !$versions_differ);</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><b></span>command line<span class="nt" style="color: navy;"></b></span>: $commands[0]<span class="nt" style="color: navy;"></br></span>\n" if (!$commands_differ);</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><b></span>directory<span class="nt" style="color: navy;"></b></span>: $directories[0]<span class="nt" style="color: navy;"></br></span>\n" if (!$directories_differ);</span>
</pre>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><b></span>version<span class="nt" style="color: navy;"></b></span>: $versions[0]\n" if (!$versions_differ);</span>
</pre>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"></p></span>" if (!$commands_differ || !$directories_differ || !$versions_differ);</span>
</pre>
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623
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637
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="html"> #$section .= '<span class="nt" style="color: navy;"><table</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">"width:100%"</span><span class="nt" style="color: navy;">></span>'."\n";</span>
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624
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638
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="html"></span>
</pre>
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625
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<td class="diff-line-num new_line" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
639
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC639" class="line" lang="html"> #$section .= '<span class="nt" style="color: navy;"><table</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"backlit2 center"</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">"width:100%"</span><span class="nt" style="color: navy;">></span>'."\n";</span>
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<td class="diff-line-num old_line" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
626
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<td class="diff-line-num new_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
640
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC640" class="line" lang="html"> $section .= '<span class="nt" style="color: navy;"><table</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"backlit2 center"</span><span class="nt" style="color: navy;">></span>'."\n";</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
627
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<td class="diff-line-num new_line old" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC627" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><tr><th></span>chain #<span class="nt" style="color: navy;"></th><th></span>burnin<span class="nt" style="color: navy;"></th><th></span>subsample<span class="nt" style="color: navy;"></th><th></span>Iterations (after burnin)<span class="nt" style="color: navy;"></th></span>";</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><tr><th></span>chain #<span class="nt" style="color: navy;"></th></span>";</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
642
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC642" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><th></span>version<span class="nt" style="color: navy;"></th></span>" if ($versions_differ);</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><th></span>burnin<span class="nt" style="color: navy;"></th><th></span>subsample<span class="nt" style="color: navy;"></th><th></span>Iterations (after burnin)<span class="nt" style="color: navy;"></th></span>";</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
628
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<td class="diff-line-num new_line" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
644
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC644" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><th></span>command line<span class="nt" style="color: navy;"></th></span>" if ($commands_differ);</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
629
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<td class="diff-line-num new_line" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
645
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC645" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><th></span>subdirectory<span class="nt" style="color: navy;"></th></span>";</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
630
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<td class="diff-line-num new_line" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
646
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC646" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><th></span>directory<span class="nt" style="color: navy;"></th></span>" if ($directories_differ);</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -634,6 +650,7 @@ sub section_analysis</td>
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<td class="diff-line-num old_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
634
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<td class="diff-line-num new_line" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
650
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC650" class="line" lang="html"><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">section</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">.=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"<</span><span class="na" style="color: teal;">tr</span><span class="nt" style="color: navy;">></span>\n";</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
635
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<td class="diff-line-num new_line" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
651
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC651" class="line" lang="html"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
636
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652
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC652" class="line" lang="html">$section .= " <span class="nt" style="color: navy;"><td></span>".($i+1)."<span class="nt" style="color: navy;"></td></span>\n";</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="html">$section .= " <span class="nt" style="color: navy;"><td></span>$versions[$i]<span class="nt" style="color: navy;"></td></span>\n" if ($versions_differ);</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
637
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<td class="diff-line-num new_line" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
654
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC654" class="line" lang="html"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
638
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<td class="diff-line-num new_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
655
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC655" class="line" lang="html">$section .= " <span class="nt" style="color: navy;"><td></span>$burnin<span class="nt" style="color: navy;"></td></span>\n";</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
639
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<td class="diff-line-num new_line" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
656
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC656" class="line" lang="html">$section .= " <span class="nt" style="color: navy;"><td></span>$subsample<span class="nt" style="color: navy;"></td></span>\n";</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -645,6 +662,7 @@ $section .= " <td>$commands[$i]</td>\n" if ($commands_differ);</td>
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<td class="diff-line-num old_line" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
645
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<td class="diff-line-num new_line" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
662
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="html">$section .= " <span class="nt" style="color: navy;"><td></span>$subdirs[$i]<span class="nt" style="color: navy;"></td></span>\n";</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
646
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<td class="diff-line-num new_line" data-linenumber="663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
663
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC663" class="line" lang="html">$section .= " <span class="nt" style="color: navy;"><td></span>$directories[$i]<span class="nt" style="color: navy;"></td></span>\n" if ($directories_differ);</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
647
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664
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="html"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
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665
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC665" class="line" lang="html"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
648
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666
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC666" class="line" lang="html">$section .= "<span class="nt" style="color: navy;"></tr></span>\n";</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
649
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<td class="diff-line-num new_line" data-linenumber="667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
667
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC667" class="line" lang="html"> }</span>
</pre>
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650
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<td class="diff-line-num new_line" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
668
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="html">$section .= "<span class="nt" style="color: navy;"></table></span>\n";</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -714,14 +732,14 @@ sub html_svg</td>
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<td class="diff-line-num old_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
714
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<td class="diff-line-num new_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
732
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<pre style="margin: 0;"> <span id="LC732" class="line" lang="html"><span class="na" style="color: teal;">sub</span> <span class="na" style="color: teal;">section_phylogeny_distribution</span></span>
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<td class="diff-line-num old_line" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
715
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<td class="diff-line-num new_line" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
733
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<pre style="margin: 0;"> <span id="LC733" class="line" lang="html"><span class="err" style="color: #a61717; background-color: #e3d2d2;">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
716
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<td class="diff-line-num new_line" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
734
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<pre style="margin: 0;"> <span id="LC734" class="line" lang="html"> <span class="na" style="color: teal;">my</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">section =</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"> </span><span class="s" style="color: #d14;">""</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="html"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">section</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">.=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"<</span><span class="na" style="color: teal;">h2</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">\"anchor\"</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">\"topology\"</span><span class="nt" style="color: navy;">></a></span>Phylogeny Distribution<span class="nt" style="color: navy;"></h2></span>\n";</span>
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<td class="diff-line-num old_line" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
717
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<td class="diff-line-num new_line" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
736
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<pre style="margin: 0;"> <span id="LC736" class="line" lang="html"> $section .= html_svg("c-levels.svg","35%","",["r_floating_picture"]);</span>
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<td class="diff-line-num old old_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
718
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<td class="diff-line-num new_line old" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC718" class="line" lang="html"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">section</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">.=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"<</span><span class="na" style="color: teal;">h2</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">\"topology\"</span><span class="nt" style="color: navy;">></span>Phylogeny Distribution<span class="nt" style="color: navy;"></a></h2></span>\n";</span>
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<td class="diff-line-num old_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
719
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737
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<pre style="margin: 0;"> <span id="LC737" class="line" lang="html"></span>
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<td class="diff-line-num old_line" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
720
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<td class="diff-line-num new_line" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
738
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<pre style="margin: 0;"> <span id="LC738" class="line" lang="html"></span>
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<td class="diff-line-num old_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
721
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<td class="diff-line-num new_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
739
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<pre style="margin: 0;"> <span id="LC739" class="line" lang="html"> $section .= html_svg("c50-tree.svg","25%","",["floating_picture"]);</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
722
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<td class="diff-line-num new_line" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
740
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<pre style="margin: 0;"> <span id="LC740" class="line" lang="html"> $section .= '<span class="nt" style="color: navy;"><table></span>'."\n";</span>
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<td class="diff-line-num old old_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
723
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<td class="diff-line-num new_line old" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC723" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><tr><td></span>Partition support: <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">\"consensus\"</span><span class="nt" style="color: navy;">></span>Summary<span class="nt" style="color: navy;"></a></td></tr></span>\n";</span>
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<td class="diff-line-num old old_line" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
724
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<td class="diff-line-num new_line old" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC724" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><tr><td><span</span> <span class="na" style="color: teal;">title=</span><span class="s" style="color: #d14;">\"How</span> <span class="na" style="color: teal;">many</span> <span class="na" style="color: teal;">partitions</span> <span class="na" style="color: teal;">are</span> <span class="na" style="color: teal;">supported</span> <span class="na" style="color: teal;">at</span> <span class="na" style="color: teal;">each</span> <span class="na" style="color: teal;">level</span> <span class="na" style="color: teal;">of</span> <span class="na" style="color: teal;">Posterior</span> <span class="na" style="color: teal;">Log</span> <span class="na" style="color: teal;">Odds</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">LOD</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)?\"</span><span class="nt" style="color: navy;">></span>Partition support graph:<span class="nt" style="color: navy;"></span></span> <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">\"c-levels.svg\"</span><span class="nt" style="color: navy;">></span>SVG<span class="nt" style="color: navy;"></a></td></tr></span>\n";</span>
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<td class="diff-line-num new old_line" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><tr><td></span>Partition support: <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">\"consensus\"</span><span class="nt" style="color: navy;">></span>Summary<span class="nt" style="color: navy;"></a></td><<span class="idiff left">td><a</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">href=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"partitions.bs\"</span></span><span class="nt" style="color: navy;"><span class="idiff">></span></span><span class="idiff">Across chains</span><span class="nt" style="color: navy;"><span class="idiff right"></a></td><</span>/tr></span>\n";</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="html"><span class="idiff left right">#</span> $section .= "<span class="nt" style="color: navy;"><tr><td><span</span> <span class="na" style="color: teal;">title=</span><span class="s" style="color: #d14;">\"How</span> <span class="na" style="color: teal;">many</span> <span class="na" style="color: teal;">partitions</span> <span class="na" style="color: teal;">are</span> <span class="na" style="color: teal;">supported</span> <span class="na" style="color: teal;">at</span> <span class="na" style="color: teal;">each</span> <span class="na" style="color: teal;">level</span> <span class="na" style="color: teal;">of</span> <span class="na" style="color: teal;">Posterior</span> <span class="na" style="color: teal;">Log</span> <span class="na" style="color: teal;">Odds</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: teal;">LOD</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)?\"</span><span class="nt" style="color: navy;">></span>Partition support graph:<span class="nt" style="color: navy;"></span></span> <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">\"c-levels.svg\"</span><span class="nt" style="color: navy;">></span>SVG<span class="nt" style="color: navy;"></a></td></tr></span>\n";</span>
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725
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743
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<pre style="margin: 0;"> <span id="LC743" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"></table></span>\n";</span>
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<td class="diff-line-num old_line" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
726
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744
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<pre style="margin: 0;"> <span id="LC744" class="line" lang="html"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
727
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745
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC745" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><table></span>\n";</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -772,7 +790,7 @@ sub section_alignment_distribution</td>
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790
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<pre style="margin: 0;"> <span id="LC790" class="line" lang="html">{</span>
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773
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<td class="diff-line-num new_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
791
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="html"> return "" if ($n_partitions == 0);</span>
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774
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792
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<pre style="margin: 0;"> <span id="LC792" class="line" lang="html"></span>
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<td class="diff-line-num old old_line" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
775
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<td class="diff-line-num new_line old" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC775" class="line" lang="html"> my $section .= "<span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">\"clear\"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;"><span class="idiff left">name=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"alignment\"</span></span><span class="nt" style="color: navy;"><span class="idiff">></span></span><span class="idiff">Alignment Distribution</span><span class="nt" style="color: navy;"><span class="idiff right"></a></span></h2></span>\n";</span>
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<td class="diff-line-num new new_line" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="html"> my $section .= "<span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">\"clear\"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;"><span class="idiff left">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"anchor\"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">name=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"alignment\"</span></span><span class="nt" style="color: navy;"><span class="idiff">></a></span></span><span class="idiff right">Alignment Distribution</span><span class="nt" style="color: navy;"></h2></span>\n";</span>
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776
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<td class="diff-line-num new_line" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
794
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<pre style="margin: 0;"> <span id="LC794" class="line" lang="html"></span>
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777
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795
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<pre style="margin: 0;"> <span id="LC795" class="line" lang="html"> for(my $i=0;$i<span class="nt" style="color: navy;"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">n_partitions</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">;$</span><span class="na" style="color: teal;">i</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">++)</span> </span>
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778
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796
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<pre style="margin: 0;"> <span id="LC796" class="line" lang="html"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -837,27 +855,23 @@ sub section_mixing</td>
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837
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855
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<pre style="margin: 0;"> <span id="LC855" class="line" lang="html">{</span>
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838
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856
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<pre style="margin: 0;"> <span id="LC856" class="line" lang="html"> my $section = "";</span>
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839
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857
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<pre style="margin: 0;"> <span id="LC857" class="line" lang="html"></span>
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<td class="diff-line-num old old_line" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
840
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<pre style="margin: 0;">-<span id="LC840" class="line" lang="html">#$section .= '<span class="nt" style="color: navy;"><object</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"r_floating_picture"</span> <span class="na" style="color: teal;">data=</span><span class="s" style="color: #d14;">"partitions.SRQ.svg"</span> <span class="na" style="color: teal;">type=</span><span class="s" style="color: #d14;">"image/svg+xml"</span> <span class="na" style="color: teal;">height=</span><span class="s" style="color: #d14;">"200pt"</span><span class="nt" style="color: navy;">></object></span>';</span>
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<td class="diff-line-num old old_line" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
841
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<td class="diff-line-num new_line old" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC841" class="line" lang="html">$section .= '<span class="nt" style="color: navy;"><img</span> <span class="na" style="color: teal;">src=</span><span class="s" style="color: #d14;">"partitions.SRQ.png"</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"r_floating_picture"</span> <span class="na" style="color: teal;">alt=</span><span class="s" style="color: #d14;">"SRQ plot for support of each partition."</span><span class="nt" style="color: navy;">/></span>';</span>
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<td class="diff-line-num old old_line" data-linenumber="842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
842
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<td class="diff-line-num new_line old" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC842" class="line" lang="html">#$section .= '<span class="nt" style="color: navy;"><object</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"r_floating_picture"</span> <span class="na" style="color: teal;">data=</span><span class="s" style="color: #d14;">"c50.SRQ.svg"</span> <span class="na" style="color: teal;">type=</span><span class="s" style="color: #d14;">"image/svg+xml"</span> <span class="na" style="color: teal;">height=</span><span class="s" style="color: #d14;">"200pt"</span><span class="nt" style="color: navy;">></object></span>';</span>
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<td class="diff-line-num old old_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
843
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<td class="diff-line-num new_line old" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC843" class="line" lang="html">#$section .= '<span class="nt" style="color: navy;"><embed</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"r_floating_picture"</span> <span class="na" style="color: teal;">src=</span><span class="s" style="color: #d14;">"c50.SRQ.svg"</span> <span class="na" style="color: teal;">type=</span><span class="s" style="color: #d14;">"image/svg+xml"</span> <span class="na" style="color: teal;">height=</span><span class="s" style="color: #d14;">"200"</span> <span class="nt" style="color: navy;">/></span>';</span>
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<td class="diff-line-num old old_line" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
844
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<td class="diff-line-num new_line old" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC844" class="line" lang="html">#$section .= '<span class="nt" style="color: navy;"><embed</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"r_floating_picture"</span> <span class="na" style="color: teal;">src=</span><span class="s" style="color: #d14;">"partitions.SRQ.svg"</span> <span class="na" style="color: teal;">type=</span><span class="s" style="color: #d14;">"image/svg+xml"</span> <span class="na" style="color: teal;">height=</span><span class="s" style="color: #d14;">"200"</span> <span class="nt" style="color: navy;">/></span>';</span>
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<td class="diff-line-num old old_line" data-linenumber="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
845
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<td class="diff-line-num new_line old" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC845" class="line" lang="html">$section .= '<span class="nt" style="color: navy;"><img</span> <span class="na" style="color: teal;">src=</span><span class="s" style="color: #d14;">"c50.SRQ.png"</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"r_floating_picture"</span> <span class="na" style="color: teal;">alt=</span><span class="s" style="color: #d14;">"SRQ plot for supprt of 50% consensus tree."</span><span class="nt" style="color: navy;">/></span>';</span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><h2><a</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">\"anchor\"</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">\"mixing\"</span><span class="nt" style="color: navy;">></a></span>Mixing<span class="nt" style="color: navy;"></h2></span>\n";</span>
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846
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859
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<pre style="margin: 0;"> <span id="LC859" class="line" lang="html"></span>
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847
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<pre style="margin: 0;">-<span id="LC847" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><h2><a</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">\"mixing\"</span><span class="nt" style="color: navy;">></span>Mixing<span class="nt" style="color: navy;"></a></h2></span>\n";</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
860
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC860" class="line" lang="html"> $section .= '<span class="nt" style="color: navy;"><table</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">"width:100%;clear:both"</span><span class="nt" style="color: navy;">><tr></span>';</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
861
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC861" class="line" lang="html"> $section .= '<span class="nt" style="color: navy;"><td</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">"vertical-align:top"</span><span class="nt" style="color: navy;">></span>';</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
848
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<td class="diff-line-num new_line" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
862
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC862" class="line" lang="html"> </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
849
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<td class="diff-line-num new_line" data-linenumber="863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
863
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC863" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><ol></span>\n";</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
850
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<td class="diff-line-num new_line old" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC850" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">\"partitions.bs\"</span><span class="nt" style="color: navy;">></span>Partition uncertainty<span class="nt" style="color: navy;"></a></li></span>\n";</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
851
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<td class="diff-line-num new_line old" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC851" class="line" lang="html"> for my $srq (@SRQ) {</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
852
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<td class="diff-line-num new_line old" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC852" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">\"$srq.SRQ.png\"</span><span class="nt" style="color: navy;">></span>SRQ plot: $srq<span class="nt" style="color: navy;"></a></li></span>\n";</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
853
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<td class="diff-line-num new_line old" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC853" class="line" lang="html"> }</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
854
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<td class="diff-line-num new_line old" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC854" class="line" lang="html"> $section .= '<span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"convergence-PP.pdf"</span><span class="nt" style="color: navy;">></span>Variation in split frequency estimates<span class="nt" style="color: navy;"></a></li></span>'."\n" if (-f "Results/convergence-PP.pdf");</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
864
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC864" class="line" lang="html"># for my $srq (@SRQ) {</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
865
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC865" class="line" lang="html"># $section .= "<span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">\"$srq.SRQ.png\"</span><span class="nt" style="color: navy;">></span>SRQ plot: $srq<span class="nt" style="color: navy;"></a></li></span>\n";</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
866
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC866" class="line" lang="html"># }</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
867
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC867" class="line" lang="html"># $section .= '<span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"convergence-PP.pdf"</span><span class="nt" style="color: navy;">></span>Variation in split frequency estimates<span class="nt" style="color: navy;"></a></li></span>'."\n" if (-f "Results/convergence-PP.pdf");</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
855
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<td class="diff-line-num new_line" data-linenumber="868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
868
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC868" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"></ol></span>\n";</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
856
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<td class="diff-line-num new_line" data-linenumber="869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
869
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC869" class="line" lang="html"> </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
857
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<td class="diff-line-num new_line" data-linenumber="870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
870
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC870" class="line" lang="html"></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
858
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<td class="diff-line-num new_line old" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC858" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><table></span>";</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
859
</td>
<td class="diff-line-num new_line old" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC859" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><tr><th></span>burnin (scalar)<span class="nt" style="color: navy;"></th><th></span>ESS (scalar)<span class="nt" style="color: navy;"></th><th></span>ESS (partition)<span class="nt" style="color: navy;"></th><th></span>ASDSF<span class="nt" style="color: navy;"></th><th></span>MSDSF<span class="nt" style="color: navy;"></th><th></span>PSRF-CI80%<span class="nt" style="color: navy;"></th><th></span>PSRF-RCF<span class="nt" style="color: navy;"></th></tr></span>";</span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
860
</td>
<td class="diff-line-num new_line old" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC860" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><tr></span>";</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
871
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC871" class="line" lang="html"> </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
872
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC872" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><p><b></span>Statistics:<span class="nt" style="color: navy;"></b></p></span>";</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
873
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC873" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><table</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">\"backlit2\"</span><span class="nt" style="color: navy;">></span>";</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="html"># $section .= "<span class="nt" style="color: navy;"><tr><th></span>burnin (scalar)<span class="nt" style="color: navy;"></th><th></span>ESS (scalar)<span class="nt" style="color: navy;"></th><th></span>ESS (partition)<span class="nt" style="color: navy;"></th><th></span>ASDSF<span class="nt" style="color: navy;"></th><th></span>MSDSF<span class="nt" style="color: navy;"></th><th></span>PSRF-CI80%<span class="nt" style="color: navy;"></th><th></span>PSRF-RCF<span class="nt" style="color: navy;"></th></tr></span>";</span>
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<pre style="margin: 0;"> <span id="LC875" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC876" class="line" lang="html"> my $burnin_before = "NA";</span>
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<pre style="margin: 0;"> <span id="LC877" class="line" lang="html"> my $min_NE = "NA";</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -868,18 +882,18 @@ $section .= '<img src="c50.SRQ.png" class="r_floating_picture" alt="SRQ plot for</td>
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<pre style="margin: 0;"> <span id="LC882" class="line" lang="html"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">min_NE =</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"> </span><span class="s" style="color: #d14;">get_value_from_file('Results/Report','Ne</span> <span class="nt" style="color: navy;">></span>=');</span>
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883
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<pre style="margin: 0;"> <span id="LC883" class="line" lang="html"> }</span>
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<pre style="margin: 0;"> <span id="LC884" class="line" lang="html"> </span>
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<pre style="margin: 0;">-<span id="LC871" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><t<span class="idiff left">d></span></span><span class="idiff">$burnin_before</span><span class="nt" style="color: navy;"><span class="idiff right"></td</span>></span>";</span>
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<pre style="margin: 0;">-<span id="LC872" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><t<span class="idiff left">d></span></span><span class="idiff">$min_NE</span><span class="nt" style="color: navy;"><span class="idiff right"></td</span>></span>";</span>
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><t<span class="idiff left">r><td><b></span></span><span class="idiff">scalar burnin</span><span class="nt" style="color: navy;"><span class="idiff"></b></td><td></span></span><span class="idiff">$burnin_before</span><span class="nt" style="color: navy;"><span class="idiff right"></td></tr</span>></span>";</span>
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><t<span class="idiff left">r><td><b></span></span><span class="idiff">scalar ESS</span><span class="nt" style="color: navy;"><span class="idiff"></b></td><td></span></span><span class="idiff">$min_NE</span><span class="nt" style="color: navy;"><span class="idiff right"></td></tr</span>></span>";</span>
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<pre style="margin: 0;"> <span id="LC887" class="line" lang="html"> my $min_NE_partition = get_value_from_file('Results/partitions.bs','min Ne =');</span>
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<pre style="margin: 0;">-<span id="LC874" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><t<span class="idiff left">d></span></span><span class="idiff">$min_NE_partition</span><span class="nt" style="color: navy;"><span class="idiff right"></td</span>></span>";</span>
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><t<span class="idiff left">r><td><b</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">title=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"Effective</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">Sample</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">Size</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">bit-vectors</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">of</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">partition</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">support</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">(</span></span><span class="na" style="color: teal;"><span class="idiff">smallest</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">)\"</span></span><span class="nt" style="color: navy;"><span class="idiff">></span></span><span class="idiff">topological ESS</span><span class="nt" style="color: navy;"><span class="idiff"></b></td><td></span></span><span class="idiff">$min_NE_partition</span><span class="nt" style="color: navy;"><span class="idiff right"></td></tr</span>></span>";</span>
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<pre style="margin: 0;"> <span id="LC889" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC890" class="line" lang="html"> my $asdsf = get_value_from_file('Results/partitions.bs','ASDSF\[min=0.100\] =');</span>
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<pre style="margin: 0;"> <span id="LC891" class="line" lang="html"> $asdsf = "NA" if (!defined($asdsf));</span>
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<pre style="margin: 0;">-<span id="LC878" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><t<span class="idiff left">d></span></span><span class="idiff">$asdsf</span><span class="nt" style="color: navy;"><span class="idiff right"></td</span>></span>";</span>
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><t<span class="idiff left">r><td><b</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">title=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"Average</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">Standard</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">Deviation</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">of</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">Split</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">Frequencies</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">\"</span></span><span class="nt" style="color: navy;"><span class="idiff">></span></span><span class="idiff">ASDSF</span><span class="nt" style="color: navy;"><span class="idiff"></b></td><td></span></span><span class="idiff">$asdsf</span><span class="nt" style="color: navy;"><span class="idiff right"></td></tr</span>></span>";</span>
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<pre style="margin: 0;"> <span id="LC893" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC894" class="line" lang="html"> my $msdsf = get_value_from_file('Results/partitions.bs','MSDSF =');</span>
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895
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<pre style="margin: 0;"> <span id="LC895" class="line" lang="html"> $msdsf = "NA" if (!defined($msdsf));</span>
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882
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<pre style="margin: 0;">-<span id="LC882" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><t<span class="idiff left">d></span></span><span class="idiff">$msdsf</span><span class="nt" style="color: navy;"><span class="idiff right"></td</span>></span>";</span>
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896
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><t<span class="idiff left">r><td><b</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">title=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"Maximum</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">Standard</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">Deviation</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">of</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">Split</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">Frequencies</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">\"</span></span><span class="nt" style="color: navy;"><span class="idiff">></span></span><span class="idiff">MSDSF</span><span class="nt" style="color: navy;"><span class="idiff"></b></td><td></span></span><span class="idiff">$msdsf</span><span class="nt" style="color: navy;"><span class="idiff right"></td></tr</span>></span>";</span>
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883
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897
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<pre style="margin: 0;"> <span id="LC897" class="line" lang="html"></span>
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884
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898
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<pre style="margin: 0;"> <span id="LC898" class="line" lang="html"> my $psrf_80 = "NA";</span>
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885
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899
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<pre style="margin: 0;"> <span id="LC899" class="line" lang="html"> my $psrf_rcf = "NA";</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -888,10 +902,9 @@ $section .= '<img src="c50.SRQ.png" class="r_floating_picture" alt="SRQ plot for</td>
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888
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902
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<pre style="margin: 0;"> <span id="LC902" class="line" lang="html"> $psrf_80 = get_value_from_file('Results/Report','PSRF-80%CI <span class="nt" style="color: navy;"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">=');</span></span>
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889
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903
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<pre style="margin: 0;"> <span id="LC903" class="line" lang="html"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">psrf_rcf =</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"> </span><span class="s" style="color: #d14;">get_value_from_file('Results/Report','PSRF-RCF</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;"><=');</span></span>
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890
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904
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<pre style="margin: 0;"> <span id="LC904" class="line" lang="html"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">}</span></span>
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891
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<pre style="margin: 0;">-<span id="LC891" class="line" lang="html"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">section</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">.=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"<</span><span class="na" style="color: teal;">t<span class="idiff left">d</span></span><span class="nt" style="color: navy;"><span class="idiff">></span></span><span class="idiff">$psrf_80</span><span class="nt" style="color: navy;"><span class="idiff right"></td</span>></span>";</span>
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892
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<pre style="margin: 0;">-<span id="LC892" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><t<span class="idiff left">d></span></span><span class="idiff">$psrf_rcf</span><span class="nt" style="color: navy;"><span class="idiff right"></td</span>></span>";</span>
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905
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="html"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">section</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">.=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"<</span><span class="na" style="color: teal;">t<span class="idiff left">r</span></span><span class="nt" style="color: navy;"><span class="idiff">><td><b></span></span><span class="idiff">PSRF CI80%</span><span class="nt" style="color: navy;"><span class="idiff"></b></td><td></span></span><span class="idiff">$psrf_80</span><span class="nt" style="color: navy;"><span class="idiff right"></td></tr</span>></span>";</span>
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<td class="diff-line-num new new_line" data-linenumber="906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><t<span class="idiff left">r><td><b></span></span><span class="idiff">PSRF RCF</span><span class="nt" style="color: navy;"><span class="idiff"></b></td><td></span></span><span class="idiff">$psrf_rcf</span><span class="nt" style="color: navy;"><span class="idiff right"></td></tr</span>></span>";</span>
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893
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907
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<pre style="margin: 0;"> <span id="LC907" class="line" lang="html"></span>
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894
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<pre style="margin: 0;">-<span id="LC894" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"></tr></span>";</span>
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895
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908
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<pre style="margin: 0;"> <span id="LC908" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"></table></span>\n";</span>
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896
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909
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<pre style="margin: 0;"> <span id="LC909" class="line" lang="html"></span>
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897
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910
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<pre style="margin: 0;"> <span id="LC910" class="line" lang="html"> ###### What file should we show for MDS?</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -916,14 +929,27 @@ $section .= '<img src="c50.SRQ.png" class="r_floating_picture" alt="SRQ plot for</td>
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916
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929
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<pre style="margin: 0;"> <span id="LC929" class="line" lang="html"> $MDS_figure_3d = "tree-3D1-1.points";</span>
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917
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930
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<pre style="margin: 0;"> <span id="LC930" class="line" lang="html"> $title = "1 chain";</span>
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<td class="diff-line-num old_line" data-linenumber="918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
918
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931
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<pre style="margin: 0;"> <span id="LC931" class="line" lang="html"> }</span>
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932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="html"> $section .= '<span class="nt" style="color: navy;"></td></span>';</span>
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<td class="diff-line-num new old_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="html">#$section .= '<span class="nt" style="color: navy;"><object</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"r_floating_picture"</span> <span class="na" style="color: teal;">data=</span><span class="s" style="color: #d14;">"partitions.SRQ.svg"</span> <span class="na" style="color: teal;">type=</span><span class="s" style="color: #d14;">"image/svg+xml"</span> <span class="na" style="color: teal;">height=</span><span class="s" style="color: #d14;">"200pt"</span><span class="nt" style="color: navy;">></object></span>';</span>
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<td class="diff-line-num new old_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
934
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC934" class="line" lang="html"> $section .= '<span class="nt" style="color: navy;"><td></span>';</span>
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<td class="diff-line-num new old_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
935
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC935" class="line" lang="html"># $section .= '<span class="nt" style="color: navy;"></td></span>';</span>
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<td class="diff-line-num new old_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
936
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC936" class="line" lang="html">#$section .= '<span class="nt" style="color: navy;"><object</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"r_floating_picture"</span> <span class="na" style="color: teal;">data=</span><span class="s" style="color: #d14;">"c50.SRQ.svg"</span> <span class="na" style="color: teal;">type=</span><span class="s" style="color: #d14;">"image/svg+xml"</span> <span class="na" style="color: teal;">height=</span><span class="s" style="color: #d14;">"200pt"</span><span class="nt" style="color: navy;">></object></span>';</span>
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<td class="diff-line-num new new_line" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
937
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC937" class="line" lang="html">#$section .= '<span class="nt" style="color: navy;"><embed</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"r_floating_picture"</span> <span class="na" style="color: teal;">src=</span><span class="s" style="color: #d14;">"c50.SRQ.svg"</span> <span class="na" style="color: teal;">type=</span><span class="s" style="color: #d14;">"image/svg+xml"</span> <span class="na" style="color: teal;">height=</span><span class="s" style="color: #d14;">"200"</span> <span class="nt" style="color: navy;">/></span>';</span>
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<td class="diff-line-num new new_line" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
938
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC938" class="line" lang="html">#$section .= '<span class="nt" style="color: navy;"><embed</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"r_floating_picture"</span> <span class="na" style="color: teal;">src=</span><span class="s" style="color: #d14;">"partitions.SRQ.svg"</span> <span class="na" style="color: teal;">type=</span><span class="s" style="color: #d14;">"image/svg+xml"</span> <span class="na" style="color: teal;">height=</span><span class="s" style="color: #d14;">"200"</span> <span class="nt" style="color: navy;">/></span>';</span>
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<td class="diff-line-num new new_line" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
939
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<pre style="margin: 0;">+<span id="LC939" class="line" lang="html"># $section .= '<span class="nt" style="color: navy;"><td></span>';</span>
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<td class="diff-line-num new old_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
940
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC940" class="line" lang="html"> $section .= '<span class="nt" style="color: navy;"><img</span> <span class="na" style="color: teal;">src=</span><span class="s" style="color: #d14;">"c50.SRQ.png"</span> <span class="na" style="color: teal;">alt=</span><span class="s" style="color: #d14;">"SRQ plot for supprt of 50% consensus tree."</span><span class="nt" style="color: navy;">/></span>';</span>
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<td class="diff-line-num new old_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
941
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC941" class="line" lang="html"> $section .= '<span class="nt" style="color: navy;"><img</span> <span class="na" style="color: teal;">src=</span><span class="s" style="color: #d14;">"partitions.SRQ.png"</span> <span class="na" style="color: teal;">alt=</span><span class="s" style="color: #d14;">"SRQ plot for support of each partition."</span><span class="nt" style="color: navy;">/></span>';</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
942
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="html"> $section .= '<span class="nt" style="color: navy;"></td></span>';</span>
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<td class="diff-line-num old_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
919
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943
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<pre style="margin: 0;"> <span id="LC943" class="line" lang="html"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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944
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="html"> $section .= '<span class="nt" style="color: navy;"></tr></table></span>';</span>
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<td class="diff-line-num new old_line" data-linenumber="920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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945
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC945" class="line" lang="html"> </span>
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920
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<td class="diff-line-num new_line" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
946
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC946" class="line" lang="html"> ###### Table of MDS versus </span>
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<td class="diff-line-num old_line" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
921
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947
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC947" class="line" lang="html"> $section .= '<span class="nt" style="color: navy;"><table</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">"width:100%;clear:both"</span><span class="nt" style="color: navy;">><tr></span>';</span>
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<td class="diff-line-num old_line" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
922
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948
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<pre style="margin: 0;"> <span id="LC948" class="line" lang="html"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
923
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<td class="diff-line-num new_line" data-linenumber="949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
949
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC949" class="line" lang="html"> $section .= '<span class="nt" style="color: navy;"><td</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">"width:40%;vertical-align:top"</span><span class="nt" style="color: navy;">></span>';</span>
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<td class="diff-line-num old_line" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
924
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<td class="diff-line-num new_line" data-linenumber="950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
950
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC950" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><h4</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">\"text-align:center\"</span><span class="nt" style="color: navy;">></span>Projection of RF distances for $title (<span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">\"https://doi.org/10.1080/10635150590946961\"</span><span class="nt" style="color: navy;">></span>Hillis et al 2005<span class="nt" style="color: navy;"></a></span>)<span class="nt" style="color: navy;"></h4></span>";</span>
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<td class="diff-line-num old_line" data-linenumber="925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
925
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<td class="diff-line-num new_line" data-linenumber="951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
951
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<pre style="margin: 0;"> <span id="LC951" class="line" lang="html"> $section .= html_svg($MDS_figure,"90%","",[]) if (defined($MDS_figure));</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
926
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<td class="diff-line-num new_line old" data-linenumber="952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC926" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">'<span class="idiff left right">file:</span>${MDS_figure_3d}.html'</span><span class="nt" style="color: navy;">></span>3D<span class="nt" style="color: navy;"></a></span>";</span>
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<td class="diff-line-num new old_line" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">'${MDS_figure_3d}.html'</span><span class="nt" style="color: navy;">></span>3D<span class="nt" style="color: navy;"></a></span>";</span>
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<td class="diff-line-num old_line" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
927
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<td class="diff-line-num new_line" data-linenumber="953" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
953
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC953" class="line" lang="html"> $section .= '<span class="nt" style="color: navy;"></td></span>';</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
928
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<td class="diff-line-num new_line" data-linenumber="954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
954
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC954" class="line" lang="html"> </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
929
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<td class="diff-line-num new_line" data-linenumber="955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
955
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC955" class="line" lang="html"> $section .= '<span class="nt" style="color: navy;"><td</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">"width:40%;vertical-align:top"</span><span class="nt" style="color: navy;">></span>';</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -944,6 +970,7 @@ $section .= '<img src="c50.SRQ.png" class="r_floating_picture" alt="SRQ plot for</td>
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<td class="diff-line-num old_line" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
944
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<td class="diff-line-num new_line" data-linenumber="970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
970
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC970" class="line" lang="html"> }</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
945
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<td class="diff-line-num new_line" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
971
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC971" class="line" lang="html"> $section .= '<span class="nt" style="color: navy;"></td></span>';</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
946
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<td class="diff-line-num new_line" data-linenumber="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
972
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC972" class="line" lang="html"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
973
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC973" class="line" lang="html"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
947
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<td class="diff-line-num new_line" data-linenumber="974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
974
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC974" class="line" lang="html"> $section .= '<span class="nt" style="color: navy;"></tr></table></span>';</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
948
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<td class="diff-line-num new_line" data-linenumber="975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
975
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC975" class="line" lang="html"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
949
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<td class="diff-line-num new_line" data-linenumber="976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
976
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC976" class="line" lang="html">my $tne_string = exec_show("pickout -n Ne <span class="nt" style="color: navy;"><</span> <span class="nt" style="color: navy;">Results</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">/</span><span class="na" style="color: teal;">partitions</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="na" style="color: teal;">bs</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">");</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -968,7 +995,7 @@ sub section_scalar_variables</td>
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<td class="diff-line-num old_line" data-linenumber="968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
968
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<td class="diff-line-num new_line" data-linenumber="995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
995
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<pre style="margin: 0;"> <span id="LC995" class="line" lang="html"><span class="err" style="color: #a61717; background-color: #e3d2d2;">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
969
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<td class="diff-line-num new_line" data-linenumber="996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
996
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<pre style="margin: 0;"> <span id="LC996" class="line" lang="html"> <span class="na" style="color: teal;">my</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">section =</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"> </span><span class="s" style="color: #d14;">""</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
970
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<td class="diff-line-num new_line" data-linenumber="997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
997
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC997" class="line" lang="html"> <span class="na" style="color: teal;">if</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">($#</span><span class="na" style="color: teal;">var_names</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">!=</span> <span class="na" style="color: teal;">-1</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">{</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
971
</td>
<td class="diff-line-num new_line old" data-linenumber="998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC971" class="line" lang="html"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">section</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">.=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"<</span><span class="na" style="color: teal;">h2</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">\"clear\"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;"><span class="idiff left">name=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"parameters\"</span></span><span class="nt" style="color: navy;"><span class="idiff">></span></span><span class="idiff">Scalar variables</span><span class="nt" style="color: navy;"><span class="idiff right"></a></span></h2></span>\n";</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
998
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC998" class="line" lang="html"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="na" style="color: teal;">section</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">.=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"<</span><span class="na" style="color: teal;">h2</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">\"clear\"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;"><span class="idiff left">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"anchor\"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">name=</span></span><span class="s" style="color: #d14;"><span class="idiff">\"parameters\"</span></span><span class="nt" style="color: navy;"><span class="idiff">></a></span></span><span class="idiff right">Scalar variables</span><span class="nt" style="color: navy;"></h2></span>\n";</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
972
</td>
<td class="diff-line-num new_line" data-linenumber="999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
999
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC999" class="line" lang="html"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
973
</td>
<td class="diff-line-num new_line" data-linenumber="1000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1000
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1000" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><table</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">\"backlit2\"</span><span class="nt" style="color: navy;">></span>\n";</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
974
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<td class="diff-line-num new_line" data-linenumber="1001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1001
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<pre style="margin: 0;"> <span id="LC1001" class="line" lang="html"> $section .= "<span class="nt" style="color: navy;"><tr><th></span>Statistic<span class="nt" style="color: navy;"></th><th></span>Median<span class="nt" style="color: navy;"></th><th</span> <span class="na" style="color: teal;">title=</span><span class="s" style="color: #d14;">\"95%</span> <span class="na" style="color: teal;">Bayesian</span> <span class="na" style="color: teal;">Credible</span> <span class="na" style="color: teal;">Interval</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\"</span><span class="nt" style="color: navy;">></span>95% BCI<span class="nt" style="color: navy;"></th><th</span> <span class="na" style="color: teal;">title=</span><span class="s" style="color: #d14;">\"Auto-Correlation</span> <span class="na" style="color: teal;">Time</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\"</span><span class="nt" style="color: navy;">></span>ACT<span class="nt" style="color: navy;"></th><th</span> <span class="na" style="color: teal;">title=</span><span class="s" style="color: #d14;">\"Effective</span> <span class="na" style="color: teal;">Sample</span> <span class="na" style="color: teal;">Size</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\"</span><span class="nt" style="color: navy;">></span>ESS<span class="nt" style="color: navy;"></th><th></span>burnin<span class="nt" style="color: navy;"></th><th</span> <span class="na" style="color: teal;">title=</span><span class="s" style="color: #d14;">\"Potential</span> <span class="na" style="color: teal;">Scale</span> <span class="na" style="color: teal;">Reduction</span> <span class="na" style="color: teal;">Factor</span> <span class="na" style="color: teal;">based</span> <span class="na" style="color: teal;">on</span> <span class="na" style="color: teal;">width</span> <span class="na" style="color: teal;">of</span> <span class="na" style="color: teal;">80</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">%</span> <span class="na" style="color: teal;">credible</span> <span class="na" style="color: teal;">interval</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\"</span><span class="nt" style="color: navy;">></span>PSRF-CI80%<span class="nt" style="color: navy;"></th><th></span>PSRF-RCF<span class="nt" style="color: navy;"></th></tr></span>\n";</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1613,7 +1640,7 @@ sub draw_alignments</td>
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<td class="diff-line-num old_line" data-linenumber="1613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1613
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<td class="diff-line-num new_line" data-linenumber="1640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1640
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<pre style="margin: 0;"> <span id="LC1640" class="line" lang="html"> }</span>
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<td class="diff-line-num old_line" data-linenumber="1614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1614
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<td class="diff-line-num new_line" data-linenumber="1641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1641
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<pre style="margin: 0;"> <span id="LC1641" class="line" lang="html"> </span>
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<td class="diff-line-num old_line" data-linenumber="1615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1615
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<td class="diff-line-num new_line" data-linenumber="1642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1642
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<pre style="margin: 0;"> <span id="LC1642" class="line" lang="html"> if (! more_recent_than("Results/$alignment-diff.html","Results/$alignment-diff.AU")) {</span>
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1616
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<td class="diff-line-num new_line old" data-linenumber="1643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1616" class="line" lang="html"> exec_show("alignment-draw Results/$alignment.fasta --scale=identity --AU Results/$alignment-diff.AU --show-ruler --color-scheme=diff[<span class="idiff left right">3</span>]+contrast > Results/$alignment-diff.html");</span>
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<td class="diff-line-num new old_line" data-linenumber="1617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1643
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<pre style="margin: 0;">+<span id="LC1643" class="line" lang="html"> exec_show("alignment-draw Results/$alignment.fasta --scale=identity --AU Results/$alignment-diff.AU --show-ruler --color-scheme=diff[<span class="idiff left right">1</span>]+contrast > Results/$alignment-diff.html");</span>
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<td class="diff-line-num old_line" data-linenumber="1617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1617
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1644
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<pre style="margin: 0;"> <span id="LC1644" class="line" lang="html"> }</span>
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<td class="diff-line-num old_line" data-linenumber="1618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1618
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<td class="diff-line-num new_line" data-linenumber="1645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1645
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<pre style="margin: 0;"> <span id="LC1645" class="line" lang="html"> }</span>
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<td class="diff-line-num old_line" data-linenumber="1619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1619
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<td class="diff-line-num new_line" data-linenumber="1646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1646
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<pre style="margin: 0;"> <span id="LC1646" class="line" lang="html"> print "done.\n";</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2253,6 +2280,43 @@ sub get_models_for_file</td>
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<td class="diff-line-num old_line" data-linenumber="2253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2253
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<td class="diff-line-num new_line" data-linenumber="2280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2280
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<pre style="margin: 0;"> <span id="LC2280" class="line" lang="html"> return [@models];</span>
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<td class="diff-line-num old_line" data-linenumber="2254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2254
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<td class="diff-line-num new_line" data-linenumber="2281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2281
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<pre style="margin: 0;"> <span id="LC2281" class="line" lang="html">}</span>
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2255
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<td class="diff-line-num new_line" data-linenumber="2282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2282
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<pre style="margin: 0;"> <span id="LC2282" class="line" lang="html"></span>
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2283
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<pre style="margin: 0;">+<span id="LC2283" class="line" lang="html">sub get_version_for_file</span>
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<td class="diff-line-num new new_line" data-linenumber="2284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2284
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<pre style="margin: 0;">+<span id="LC2284" class="line" lang="html">{</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2285
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<pre style="margin: 0;">+<span id="LC2285" class="line" lang="html"> my $file = shift;</span>
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<td class="diff-line-num new new_line" data-linenumber="2286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2286
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<pre style="margin: 0;">+<span id="LC2286" class="line" lang="html"> my $version = get_header_attribute("VERSION",[$file]);</span>
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2287
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<pre style="margin: 0;">+<span id="LC2287" class="line" lang="html"> $version = (split /\s+/,$version)[0];</span>
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2288
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<pre style="margin: 0;">+<span id="LC2288" class="line" lang="html"> return $version;</span>
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2289
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<pre style="margin: 0;">+<span id="LC2289" class="line" lang="html">}</span>
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2290
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<pre style="margin: 0;">+<span id="LC2290" class="line" lang="html"></span>
</pre>
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2291
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<pre style="margin: 0;">+<span id="LC2291" class="line" lang="html">sub get_version_for_run_file</span>
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<td class="diff-line-num new new_line" data-linenumber="2292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2292
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<pre style="margin: 0;">+<span id="LC2292" class="line" lang="html">{</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2293
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<pre style="margin: 0;">+<span id="LC2293" class="line" lang="html"> my $file = shift;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2294
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2294" class="line" lang="html"> my $j = get_json_from_file($file);</span>
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<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2295
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2295" class="line" lang="html"> return ${$j}{'program'}{'version'};</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2296
</td>
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<pre style="margin: 0;">+<span id="LC2296" class="line" lang="html">}</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2297
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2297" class="line" lang="html"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2298
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<pre style="margin: 0;">+<span id="LC2298" class="line" lang="html">sub get_all_versions</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2299
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2299" class="line" lang="html">{</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2300
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2300" class="line" lang="html"> return [] if ($#out_files == -1);</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2301
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2301" class="line" lang="html"> my @versions;</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2302
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2302" class="line" lang="html"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2303
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2303" class="line" lang="html"> if (!@run_files)</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2304
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2304" class="line" lang="html"> {</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2305
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2305" class="line" lang="html"> foreach my $out_file (@out_files)</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2306
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2306" class="line" lang="html"> {</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2307
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2307" class="line" lang="html"> push @versions, get_version_for_file($out_file);</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2308
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2308" class="line" lang="html"> }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2309
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2309" class="line" lang="html"> }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2310
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2310" class="line" lang="html"> else</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2311
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2311" class="line" lang="html"> {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2312
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2312" class="line" lang="html"> foreach my $run_file (@run_files)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2313
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2313" class="line" lang="html"> {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2314
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2314" class="line" lang="html"> push @versions, get_version_for_run_file($run_file);</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2315
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2315" class="line" lang="html"> }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2316
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2316" class="line" lang="html"> }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2317
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<pre style="margin: 0;">+<span id="LC2317" class="line" lang="html"> return @versions;</span>
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2318
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<pre style="margin: 0;">+<span id="LC2318" class="line" lang="html">}</span>
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2319
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<pre style="margin: 0;">+<span id="LC2319" class="line" lang="html"></span>
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2256
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2320
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<pre style="margin: 0;"> <span id="LC2320" class="line" lang="html">sub get_models</span>
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2257
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2321
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<pre style="margin: 0;"> <span id="LC2321" class="line" lang="html">{</span>
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2258
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2322
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<pre style="margin: 0;"> <span id="LC2322" class="line" lang="html"> my $name1 = shift;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2882,8 +2946,8 @@ sub tree_MDS</td>
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2882
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2946
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<pre style="margin: 0;"> <span id="LC2946" class="line" lang="html"> my $outfile = "Results/tree-1-2.svg";</span>
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<td class="diff-line-num old_line" data-linenumber="2883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2883
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<td class="diff-line-num new_line" data-linenumber="2947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2947
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<pre style="margin: 0;"> <span id="LC2947" class="line" lang="html"> if (! more_recent_than($outfile, $tf1) || ! more_recent_than($outfile, $tf2))</span>
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2884
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<td class="diff-line-num new_line" data-linenumber="2948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2948
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<pre style="margin: 0;"> <span id="LC2948" class="line" lang="html"> {</span>
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2885
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<pre style="margin: 0;">-<span id="LC2885" class="line" lang="html"> my $L1 = min([$N, <span class="idiff left right">get_n_lines($tf1)-$burnin</span>]);</span>
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2886
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<pre style="margin: 0;">-<span id="LC2886" class="line" lang="html"> my $L2 = min([$N, <span class="idiff left right">get_n_lines($tf2)-$burnin</span>]);</span>
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<td class="diff-line-num new old_line" data-linenumber="2887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2949
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<pre style="margin: 0;">+<span id="LC2949" class="line" lang="html"> my $L1 = min([$N, <span class="idiff left right">int((get_n_lines($tf1)-$burnin)/$subsample)</span>]);</span>
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<td class="diff-line-num new new_line" data-linenumber="2950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2950
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<pre style="margin: 0;">+<span id="LC2950" class="line" lang="html"> my $L2 = min([$N, <span class="idiff left right">int((get_n_lines($tf2)-$burnin)/$subsample)</span>]);</span>
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2887
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2951
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<pre style="margin: 0;"> <span id="LC2951" class="line" lang="html"> my $matfile = "Results/tree-1-2.M";</span>
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2888
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2952
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<pre style="margin: 0;"> <span id="LC2952" class="line" lang="html"> # print "L1 = $L1 L2 = $L2\n";</span>
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<td class="diff-line-num old_line" data-linenumber="2889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2889
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2953
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<pre style="margin: 0;"> <span id="LC2953" class="line" lang="html"> exec_show("trees-distances matrix --max=$N --jitter=0.3 $subsample_string $skip $tf1 $tf2 > $matfile");</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2904,9 +2968,9 @@ sub tree_MDS</td>
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2904
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2968
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<pre style="margin: 0;"> <span id="LC2968" class="line" lang="html"> my $tf2 = $tree_files[1];</span>
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2905
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2969
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<pre style="margin: 0;"> <span id="LC2969" class="line" lang="html"> my $tf3 = $tree_files[2];</span>
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2906
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2970
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<pre style="margin: 0;"> <span id="LC2970" class="line" lang="html"> my $N = 400;</span>
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2907
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<pre style="margin: 0;">-<span id="LC2907" class="line" lang="html"> my $L1 = min([$N, <span class="idiff left right">get_n_lines($tf1)-$burnin</span>]);</span>
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2908
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<pre style="margin: 0;">-<span id="LC2908" class="line" lang="html"> my $L2 = min([$N, <span class="idiff left right">get_n_lines($tf2)-$burnin</span>]);</span>
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2909
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<pre style="margin: 0;">-<span id="LC2909" class="line" lang="html"> my $L3 = min([$N, <span class="idiff left right">get_n_lines($tf3)-$burnin</span>]);</span>
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2971
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<pre style="margin: 0;">+<span id="LC2971" class="line" lang="html"> my $L1 = min([$N, <span class="idiff left right">int((get_n_lines($tf1)-$burnin)/$subsample)</span>]);</span>
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2972
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<pre style="margin: 0;">+<span id="LC2972" class="line" lang="html"> my $L2 = min([$N, <span class="idiff left right">int((get_n_lines($tf2)-$burnin)/$subsample)</span>]);</span>
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<pre style="margin: 0;">+<span id="LC2973" class="line" lang="html"> my $L3 = min([$N, <span class="idiff left right">int((get_n_lines($tf3)-$burnin)/$subsample)</span>]);</span>
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<pre style="margin: 0;"> <span id="LC2974" class="line" lang="html"> my $matfile = "Results/tree-1-2-3.M";</span>
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<pre style="margin: 0;"> <span id="LC2975" class="line" lang="html"> my $outfile = "Results/tree-1-2-3.svg";</span>
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<pre style="margin: 0;"> <span id="LC2976" class="line" lang="html"># print "L1 = $L1 L2 = $L2\n";</span>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/e73664112c1ff560964d8b60a4ba295719eebc05#e0eb72319dafa1e48cc1ff017dd55138b7106de3"><strong>src/alignment/alignment-constraint.H</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef ALIGNMENT_CONSTRAINT_H</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define ALIGNMENT_CONSTRAINT_H</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Copyright (C) 2004-2007,2009 Benjamin Redelings</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -48,3 +50,5 @@ std::vector< std::pair<int,int> > get_y_ranges_for_band(int D,</td>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="c"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">get_yboundaries_from_pins</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">I</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">J</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">pins</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">boundaries_intersection</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>&</span><span class="p">,</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>&</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/e73664112c1ff560964d8b60a4ba295719eebc05#c20d0a06cb220addaa5dc6796e09bb79ab929ba2"><strong>src/bali-phy.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -533,7 +533,8 @@ int main(int argc,char* argv[])</td>
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="cpp"> <span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"subdirectory"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dir_name</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="cpp"> <span class="n" style="color: #333;">files</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">init_files</span><span class="p">(</span><span class="n" style="color: #333;">proc_id</span><span class="p">,</span> <span class="n" style="color: #333;">dir_name</span><span class="p">,</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="cpp"> <span class="n" style="color: #333;">loggers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">construct_loggers</span><span class="p">(</span><span class="n" style="color: #333;">M</span><span class="p">,</span> <span class="n" style="color: #333;">subsample</span><span class="p">,</span> <span class="n" style="color: #333;">Rao_Blackwellize</span><span class="p">,</span> <span class="n" style="color: #333;">proc_id</span><span class="p">,</span> <span class="n" style="color: #333;">dir_name</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="cpp"> <span class="n" style="color: #333;">write_initial_alignments</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">M</span><span class="p">,</span> <span class="n" style="color: #333;">proc_id</span><span class="p">,</span> <span class="n" style="color: #333;">dir_name</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"align"</span><span class="p">))</span> <span class="n" style="color: #333;">write_initial_alignments</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">proc_id</span><span class="p">,</span> <span class="n" style="color: #333;">dir_name</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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540
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="cpp"> <span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">shared_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ostream</span><span class="p">(</span><span class="n" style="color: #333;">cout</span><span class="p">.</span><span class="n" style="color: #333;">rdbuf</span><span class="p">())));</span></span>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/e73664112c1ff560964d8b60a4ba295719eebc05#33e83749497034e5ac312f2678d52d0f6a7f7d55"><strong>src/builtins/SModel.cc</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1110,7 +1110,8 @@ namespace substitution {</td>
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1110
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1110
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<pre style="margin: 0;"> <span id="LC1110" class="line" lang="cpp"> <span class="n" style="color: #333;">log_double_t</span> <span class="n" style="color: #333;">calc_root_probability_SEV</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Likelihood_Cache_Branch</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">LCB1</span><span class="p">,</span></span>
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1111
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1111
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<pre style="margin: 0;"> <span id="LC1111" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Likelihood_Cache_Branch</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">LCB2</span><span class="p">,</span></span>
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1112
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1112
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<pre style="margin: 0;"> <span id="LC1112" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Likelihood_Cache_Branch</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">LCB3</span><span class="p">,</span></span>
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1113
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<pre style="margin: 0;">-<span id="LC1113" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Matrix</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">F</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1113" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Matrix</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">F</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1114" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">counts</span><span class="p">);</span></span>
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1115
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<pre style="margin: 0;"> <span id="LC1115" class="line" lang="cpp"><span class="p">}</span></span>
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1116
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<pre style="margin: 0;"> <span id="LC1116" class="line" lang="cpp"></span>
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1116
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1117
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<pre style="margin: 0;"> <span id="LC1117" class="line" lang="cpp"><span class="k" style="font-weight: 600;">extern</span> <span class="s" style="color: #d14;">"C"</span> <span class="n" style="color: #333;">closure</span> <span class="n" style="color: #333;">builtin_function_calc_root_probability</span><span class="p">(</span><span class="n" style="color: #333;">OperationArgs</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">Args</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1139,11 +1140,13 @@ extern "C" closure builtin_function_calc_root_probability_SEV(OperationArgs& Arg</td>
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1139
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1140
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<pre style="margin: 0;"> <span id="LC1140" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">arg1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Args</span><span class="p">.</span><span class="n" style="color: #333;">evaluate</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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1140
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1141
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<pre style="margin: 0;"> <span id="LC1141" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">arg2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Args</span><span class="p">.</span><span class="n" style="color: #333;">evaluate</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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1141
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<pre style="margin: 0;"> <span id="LC1142" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">arg3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Args</span><span class="p">.</span><span class="n" style="color: #333;">evaluate</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1143" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">arg4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Args</span><span class="p">.</span><span class="n" style="color: #333;">evaluate</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1144" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1145" class="line" lang="cpp"> <span class="n" style="color: #333;">log_double_t</span> <span class="n" style="color: #333;">Pr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">substitution</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">calc_root_probability_SEV</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">arg0</span><span class="p">.</span><span class="n" style="color: #333;">as_</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Likelihood_Cache_Branch</span><span class="o" style="font-weight: 600;">></span><span class="p">(),</span></span>
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<pre style="margin: 0;"> <span id="LC1146" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">arg1</span><span class="p">.</span><span class="n" style="color: #333;">as_</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Likelihood_Cache_Branch</span><span class="o" style="font-weight: 600;">></span><span class="p">(),</span></span>
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<pre style="margin: 0;"> <span id="LC1147" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">arg2</span><span class="p">.</span><span class="n" style="color: #333;">as_</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Likelihood_Cache_Branch</span><span class="o" style="font-weight: 600;">></span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC1146" class="line" lang="cpp"> <span class="n" style="color: #333;">arg3</span><span class="p">.</span><span class="n" style="color: #333;">as_</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Box</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Matrix</span><span class="o" style="font-weight: 600;">>></span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC1148" class="line" lang="cpp"> <span class="n" style="color: #333;">arg3</span><span class="p">.</span><span class="n" style="color: #333;">as_</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Box</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Matrix</span><span class="o" style="font-weight: 600;">>></span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC1149" class="line" lang="cpp"> <span class="n" style="color: #333;">arg4</span><span class="p">.</span><span class="n" style="color: #333;">as_</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>></span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC1150" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">{</span><span class="n" style="color: #333;">Pr</span><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC1151" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1152" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,7 +12,12 @@ int OperationArgs::reg_for_slot(int slot) const</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">OperationArgs</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">n_args</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">current_closure</span><span class="p">().</span><span class="n" style="color: #333;">exp</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();}</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">expression_ref</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">OperationArgs</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reference</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">slot</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">current_closure</span><span class="p">().</span><span class="n" style="color: #333;">exp</span><span class="p">.</span><span class="n" style="color: #333;">sub</span><span class="p">()[</span><span class="n" style="color: #333;">slot</span><span class="p">];}</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">expression_ref</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">OperationArgs</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reference</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">slot</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">slot</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">slot</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">current_closure</span><span class="p">().</span><span class="n" style="color: #333;">exp</span><span class="p">.</span><span class="n" style="color: #333;">sub</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">current_closure</span><span class="p">().</span><span class="n" style="color: #333;">exp</span><span class="p">.</span><span class="n" style="color: #333;">sub</span><span class="p">()[</span><span class="n" style="color: #333;">slot</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">closure</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">OperationArgs</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">evaluate_slot_to_closure</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">slot</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/e73664112c1ff560964d8b60a4ba295719eebc05#65b7ddf0e798fdf9c7be21320e917f152ca95966"><strong>src/dp/dp-matrix.H</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -119,17 +119,9 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">forward_first_cell</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">forward_cell</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// Compute the forward probabilities for a square</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">forward_square_first</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">forward_square</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">forward_square</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// Compute the forward probabilities for a square</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// Compute the forward probabilities between y1(x) and y2(x)</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">forward_band</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">boundaries</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// compute FP for entire matrix, with some points on path pinned</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">forward_constrained</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>&</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// Sample a path from the HMM</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sample_path</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="c"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -141,21 +133,6 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">/// 2D Dynamic Programming Matrix for chains which only emit or don't emit</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">DPmatrixNoEmit</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">public</span> <span class="n" style="color: #333;">DPmatrix</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// Compute the forward probabilities for a cell</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">forward_cell</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="c"> <span class="n" style="color: #333;">log_double_t</span> <span class="n" style="color: #333;">path_Q_subst</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>&</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="c"> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">DPmatrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DPmatrix</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">DPmatrixNoEmit</span><span class="p">()</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">/// 2D Dynamic Programming Matrix for chains which emit different things</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">DPmatrixEmit</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">public</span> <span class="n" style="color: #333;">DPmatrix</span> <span class="p">{</span></span>
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161
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="c"><span class="n" style="color: #333;">protected</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -202,7 +179,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">/// 2D Dynamic Programming matrix with no constraints on states at each cell</span></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">DPmatrixSimple</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">public</span> <span class="n" style="color: #333;">DPmatrixEmit</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">DPmatrixSimple</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff right">final</span></span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">public</span> <span class="n" style="color: #333;">DPmatrixEmit</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">forward_cell</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -214,7 +191,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">/// Dynamic Programming matrix with constraints on the states</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">DPmatrixConstrained</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">public</span> <span class="n" style="color: #333;">DPmatrixEmit</span> </span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">DPmatrixConstrained</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff right">final</span></span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">public</span> <span class="n" style="color: #333;">DPmatrixEmit</span> </span>
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">order_of_computation</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">allowed_states</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -233,8 +210,6 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">clear_cell</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">forward_cell</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">);</span></span>
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">prune</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="c"> <span class="n" style="color: #333;">DPmatrixConstrained</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HMM</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">M</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="c"> <span class="n" style="color: #333;">EmissionProbs</span><span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">d1</span><span class="p">,</span></span>
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="c"> <span class="n" style="color: #333;">EmissionProbs</span><span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">d2</span><span class="p">,</span> </span>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/e73664112c1ff560964d8b60a4ba295719eebc05#4478b68e32aa01051ad81e4f640ceda3a06b49c3"><strong>src/dp/dp-matrix.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -113,34 +113,6 @@ inline void DPmatrix::forward_first_cell(int i2,int j2)</td>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"><span class="p">}</span> </span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">DPmatrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">forward_square_first</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x1</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y1</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x2</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y2</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">x1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">y1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">x1</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">x2</span> <span class="n" style="color: #333;">or</span> <span class="n" style="color: #333;">y1</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">y2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">x2</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size1</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size2</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Since we are using M(0,0) instead of S(0,0), we need to run only the silent states at (0,0)</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// We can only use non-silent states at (0,0) to simulate S</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// clear left border</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">y1</span><span class="p">;</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">y2</span><span class="p">;</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">clear_cell</span><span class="p">(</span><span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="cpp"></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// forward first row, with exception for S(0,0)</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="cpp"> <span class="n" style="color: #333;">clear_cell</span><span class="p">(</span><span class="n" style="color: #333;">x1</span><span class="p">,</span><span class="n" style="color: #333;">y1</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="cpp"> <span class="n" style="color: #333;">forward_first_cell</span><span class="p">(</span><span class="n" style="color: #333;">x1</span><span class="p">,</span><span class="n" style="color: #333;">y1</span><span class="p">);</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">y1</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">y2</span><span class="p">;</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="cpp"> <span class="n" style="color: #333;">forward_cell</span><span class="p">(</span><span class="n" style="color: #333;">x1</span><span class="p">,</span><span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="cpp"></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// forward other rows</span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">x2</span><span class="p">;</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">clear_cell</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">y1</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">y1</span><span class="p">;</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">y2</span><span class="p">;</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">forward_cell</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">DPmatrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">forward_band</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">yboundaries</span><span class="p">)</span> </span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// note: (x,y) is located at (x+1,y+1) in the matrix.</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -207,27 +179,6 @@ void DPmatrix::forward_band(const vector< pair<int,int> >& yboundaries)</td>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="cpp"> <span class="n" style="color: #333;">compute_Pr_sum_all_paths</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="cpp"><span class="p">}</span></span>
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">DPmatrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">forward_square</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x1</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y1</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x2</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y2</span><span class="p">)</span> <span class="p">{</span></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">x1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">y1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">x1</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">x2</span> <span class="n" style="color: #333;">or</span> <span class="n" style="color: #333;">y1</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">y2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">x2</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size1</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size2</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Since we are using M(0,0) instead of S(0,0), we need to run only the silent states at (0,0)</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// We can only use non-silent states at (0,0) to simulate S</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// clear left border</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">y1</span><span class="p">;</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">y2</span><span class="p">;</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;">clear_cell</span><span class="p">(</span><span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">x1</span><span class="p">;</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">x2</span><span class="p">;</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="cpp"> <span class="n" style="color: #333;">clear_cell</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">y1</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">y1</span><span class="p">;</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">y2</span><span class="p">;</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="cpp"> <span class="n" style="color: #333;">forward_cell</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">DPmatrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">compute_Pr_sum_all_paths</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">I</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size1</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -244,50 +195,6 @@ void DPmatrix::compute_Pr_sum_all_paths()</td>
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">Pr_total</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mf" style="color: #099;">1.0</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">DPmatrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">forward_square</span><span class="p">()</span> </span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">I</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size1</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">J</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size2</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="cpp"> <span class="n" style="color: #333;">forward_square_first</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">I</span><span class="p">,</span><span class="n" style="color: #333;">J</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="cpp"> <span class="n" style="color: #333;">compute_Pr_sum_all_paths</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// FIXME - fix up pins for new matrix coordinates</span></span>
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">DPmatrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">forward_constrained</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">pins</span><span class="p">)</span> </span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">I</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size1</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">J</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size2</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="cpp"></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">yboundaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_yboundaries_from_pins</span><span class="p">(</span><span class="n" style="color: #333;">I</span><span class="p">,</span> <span class="n" style="color: #333;">J</span><span class="p">,</span> <span class="n" style="color: #333;">pins</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pins</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pins</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="cpp"> <span class="n" style="color: #333;">forward_band</span><span class="p">(</span><span class="n" style="color: #333;">yboundaries</span><span class="p">);</span></span>
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271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> </span>
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274
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="cpp"> <span class="n" style="color: #333;">forward_square</span><span class="p">();</span></span>
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275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> </span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="cpp"> <span class="p">{</span></span>
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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Propogate from S to first pin</span></span>
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278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="cpp"> <span class="n" style="color: #333;">forward_square_first</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">y</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Propogate from first pin to other pins (if any)</span></span>
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="cpp"> <span class="n" style="color: #333;">forward_square</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">y</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="n" style="color: #333;">y</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="cpp"> <span class="n" style="color: #333;">forward_square</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">y</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">I</span><span class="p">,</span><span class="n" style="color: #333;">J</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="cpp"> <span class="n" style="color: #333;">compute_Pr_sum_all_paths</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp"><span class="n" style="color: #333;">log_double_t</span> <span class="n" style="color: #333;">DPmatrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path_P</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">path</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> </span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">I</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size1</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -415,60 +322,6 @@ DPmatrix::DPmatrix(int i1,</td>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">)(</span><span class="n" style="color: #333;">I</span><span class="p">,</span><span class="n" style="color: #333;">J</span><span class="p">,</span><span class="n" style="color: #333;">state1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">DPmatrixNoEmit</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">forward_cell</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i2</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j2</span><span class="p">)</span> </span>
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419
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="cpp"><span class="p">{</span> </span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">i2</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">i2</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size1</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">j2</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">j2</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size2</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// determine initial scale for this cell</span></span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="cpp"> <span class="n" style="color: #333;">scale</span><span class="p">(</span><span class="n" style="color: #333;">i2</span><span class="p">,</span><span class="n" style="color: #333;">j2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">(</span><span class="n" style="color: #333;">i2</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">j2</span><span class="p">),</span> <span class="n" style="color: #333;">max</span><span class="p">(</span> <span class="n" style="color: #333;">scale</span><span class="p">(</span><span class="n" style="color: #333;">i2</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">j2</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="n" style="color: #333;">scale</span><span class="p">(</span><span class="n" style="color: #333;">i2</span><span class="p">,</span><span class="n" style="color: #333;">j2</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">)</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maximum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s2</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">s2</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">n_dp_states</span><span class="p">();</span><span class="n" style="color: #333;">s2</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> </span>
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">S2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dp_order</span><span class="p">(</span><span class="n" style="color: #333;">s2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//--- Get (i1,j1) from (i2,j2) and S2</span></span>
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">di</span><span class="p">(</span><span class="n" style="color: #333;">S2</span><span class="p">))</span> <span class="n" style="color: #333;">i1</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dj</span><span class="p">(</span><span class="n" style="color: #333;">S2</span><span class="p">))</span> <span class="n" style="color: #333;">j1</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//--- compute arrival probability ----</span></span>
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">MAX</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_dp_states</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">not</span> <span class="n" style="color: #333;">di</span><span class="p">(</span><span class="n" style="color: #333;">S2</span><span class="p">)</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">not</span> <span class="n" style="color: #333;">dj</span><span class="p">(</span><span class="n" style="color: #333;">S2</span><span class="p">))</span> <span class="n" style="color: #333;">MAX</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s1</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">s1</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">MAX</span><span class="p">;</span><span class="n" style="color: #333;">s1</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">S1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dp_order</span><span class="p">(</span><span class="n" style="color: #333;">s1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">)(</span><span class="n" style="color: #333;">i1</span><span class="p">,</span><span class="n" style="color: #333;">j1</span><span class="p">,</span><span class="n" style="color: #333;">S1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">GQ</span><span class="p">(</span><span class="n" style="color: #333;">S1</span><span class="p">,</span><span class="n" style="color: #333;">S2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC449" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// rescale result to scale of this cell</span></span>
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">(</span><span class="n" style="color: #333;">i1</span><span class="p">,</span><span class="n" style="color: #333;">j1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">scale</span><span class="p">(</span><span class="n" style="color: #333;">i2</span><span class="p">,</span><span class="n" style="color: #333;">j2</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">pow2</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">(</span><span class="n" style="color: #333;">i1</span><span class="p">,</span><span class="n" style="color: #333;">j1</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">scale</span><span class="p">(</span><span class="n" style="color: #333;">i2</span><span class="p">,</span><span class="n" style="color: #333;">j2</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// record maximum</span></span>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">maximum</span><span class="p">)</span> <span class="n" style="color: #333;">maximum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">temp</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC456" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// store the result</span></span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">)(</span><span class="n" style="color: #333;">i2</span><span class="p">,</span><span class="n" style="color: #333;">j2</span><span class="p">,</span><span class="n" style="color: #333;">S2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">temp</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//------- if exponent is too high or too low, rescale ------//</span></span>
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maximum</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">fp_scale</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">hi_cutoff</span> <span class="n" style="color: #333;">or</span> <span class="p">(</span><span class="n" style="color: #333;">maximum</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">maximum</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">fp_scale</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">lo_cutoff</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">logs</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">log2</span><span class="p">(</span><span class="n" style="color: #333;">maximum</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pow2</span><span class="p">(</span><span class="n" style="color: #333;">logs</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">S2</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">S2</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">n_dp_states</span><span class="p">();</span><span class="n" style="color: #333;">S2</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> </span>
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">)(</span><span class="n" style="color: #333;">i2</span><span class="p">,</span><span class="n" style="color: #333;">j2</span><span class="p">,</span><span class="n" style="color: #333;">S2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">scale_</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="cpp"> <span class="n" style="color: #333;">scale</span><span class="p">(</span><span class="n" style="color: #333;">i2</span><span class="p">,</span><span class="n" style="color: #333;">j2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">logs</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="cpp"><span class="p">}</span> </span>
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sum</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">valarray</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">sum</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -490,17 +343,8 @@ log_double_t DPmatrixEmit::path_Q_subst(const vector<int>& path) const</td>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dj</span><span class="p">(</span><span class="n" style="color: #333;">state2</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp"> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sub</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">di</span><span class="p">(</span><span class="n" style="color: #333;">state2</span><span class="p">)</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">dj</span><span class="p">(</span><span class="n" style="color: #333;">state2</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="cpp"> <span class="n" style="color: #333;">sub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">emitMM</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">j</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">di</span><span class="p">(</span><span class="n" style="color: #333;">state2</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="cpp"> <span class="n" style="color: #333;">sub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">emitM_</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">j</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dj</span><span class="p">(</span><span class="n" style="color: #333;">state2</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="cpp"> <span class="n" style="color: #333;">sub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">emit_M</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">j</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="cpp"> <span class="n" style="color: #333;">sub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">emit__</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">j</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC503" class="line" lang="cpp"> <span class="n" style="color: #333;">P_sub</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">sub</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp"> <span class="n" style="color: #333;">P_sub</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">emitMM</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">j</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">size1</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">size2</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">P_sub</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Pr_extra_subst</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -606,18 +450,8 @@ void DPmatrixSimple::forward_cell(int i2,int j2)</td>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">)(</span><span class="n" style="color: #333;">i1</span><span class="p">,</span><span class="n" style="color: #333;">j1</span><span class="p">,</span><span class="n" style="color: #333;">S1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">GQ</span><span class="p">(</span><span class="n" style="color: #333;">S1</span><span class="p">,</span><span class="n" style="color: #333;">S2</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//--- Include Emission Probability----</span></span>
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<pre style="margin: 0;">-<span id="LC609" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sub</span><span class="p">;</span></span>
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610
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i1</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">i2</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">j1</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">j2</span><span class="p">)</span></span>
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611
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<pre style="margin: 0;">-<span id="LC611" class="line" lang="cpp"> <span class="n" style="color: #333;">sub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">emitMM</span><span class="p">(</span><span class="n" style="color: #333;">i2</span><span class="p">,</span><span class="n" style="color: #333;">j2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC612" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i1</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">i2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC613" class="line" lang="cpp"> <span class="n" style="color: #333;">sub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">emitM_</span><span class="p">(</span><span class="n" style="color: #333;">i2</span><span class="p">,</span><span class="n" style="color: #333;">j2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC614" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">j1</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">j2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC615" class="line" lang="cpp"> <span class="n" style="color: #333;">sub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">emit_M</span><span class="p">(</span><span class="n" style="color: #333;">i2</span><span class="p">,</span><span class="n" style="color: #333;">j2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC616" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="c1" style="color: #998; font-style: italic;">// silent state - nothing emitted</span></span>
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<pre style="margin: 0;">-<span id="LC617" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC618" class="line" lang="cpp"> <span class="n" style="color: #333;">sub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">emit__</span><span class="p">(</span><span class="n" style="color: #333;">i2</span><span class="p">,</span><span class="n" style="color: #333;">j2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC619" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC620" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">sub</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">emitMM</span><span class="p">(</span><span class="n" style="color: #333;">i2</span><span class="p">,</span><span class="n" style="color: #333;">j2</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// rescale result to scale of this cell</span></span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">(</span><span class="n" style="color: #333;">i1</span><span class="p">,</span><span class="n" style="color: #333;">j1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">scale</span><span class="p">(</span><span class="n" style="color: #333;">i2</span><span class="p">,</span><span class="n" style="color: #333;">j2</span><span class="p">))</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -687,17 +521,8 @@ inline void DPmatrixConstrained::forward_cell(int i2,int j2)</td>
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//--- Include Emission Probability----</span></span>
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<pre style="margin: 0;">-<span id="LC690" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sub</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i1</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">i2</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">j1</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">j2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC692" class="line" lang="cpp"> <span class="n" style="color: #333;">sub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">emitMM</span><span class="p">(</span><span class="n" style="color: #333;">i2</span><span class="p">,</span><span class="n" style="color: #333;">j2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC693" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i1</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">i2</span><span class="p">)</span></span>
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694
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<pre style="margin: 0;">-<span id="LC694" class="line" lang="cpp"> <span class="n" style="color: #333;">sub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">emitM_</span><span class="p">(</span><span class="n" style="color: #333;">i2</span><span class="p">,</span><span class="n" style="color: #333;">j2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC695" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">j1</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">j2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC696" class="line" lang="cpp"> <span class="n" style="color: #333;">sub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">emit_M</span><span class="p">(</span><span class="n" style="color: #333;">i2</span><span class="p">,</span><span class="n" style="color: #333;">j2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC697" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="c1" style="color: #998; font-style: italic;">// silent state - nothing emitted</span></span>
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<pre style="margin: 0;">-<span id="LC698" class="line" lang="cpp"> <span class="n" style="color: #333;">sub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">emit__</span><span class="p">(</span><span class="n" style="color: #333;">i2</span><span class="p">,</span><span class="n" style="color: #333;">j2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC699" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC700" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">sub</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="cpp"> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">emitMM</span><span class="p">(</span><span class="n" style="color: #333;">i2</span><span class="p">,</span><span class="n" style="color: #333;">j2</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// rescale result to scale of this cell</span></span>
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">(</span><span class="n" style="color: #333;">i1</span><span class="p">,</span><span class="n" style="color: #333;">j1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">scale</span><span class="p">(</span><span class="n" style="color: #333;">i2</span><span class="p">,</span><span class="n" style="color: #333;">j2</span><span class="p">))</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -880,37 +705,6 @@ int DPmatrixConstrained::order_of_computation() const {</td>
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<pre style="margin: 0;"> <span id="LC705" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC706" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC707" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC883" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">DPmatrixConstrained</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">prune</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC884" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC885" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">abort</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC886" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC887" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">order1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">order_of_computation</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC888" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC889" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// For column</span></span>
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<pre style="margin: 0;">-<span id="LC890" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">allowed_states</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC891" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC892" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// and for each allowed state in that column</span></span>
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<pre style="margin: 0;">-<span id="LC893" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">allowed_states</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">s2</span><span class="o" style="font-weight: 600;">--</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC894" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC895" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// FIXME! this assumes that dj(s2) is true.</span></span>
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<pre style="margin: 0;">-<span id="LC896" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC897" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// check to see whether any states in the previous column are connected to it</span></span>
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<pre style="margin: 0;">-<span id="LC898" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">used</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC899" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">s1</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">allowed_states</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">not</span> <span class="n" style="color: #333;">used</span><span class="p">;</span><span class="n" style="color: #333;">s1</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC900" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">connected</span><span class="p">(</span><span class="n" style="color: #333;">allowed_states</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="n" style="color: #333;">s1</span><span class="p">],</span><span class="n" style="color: #333;">allowed_states</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">][</span><span class="n" style="color: #333;">s2</span><span class="p">]))</span></span>
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<pre style="margin: 0;">-<span id="LC901" class="line" lang="cpp"> <span class="n" style="color: #333;">used</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC902" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC903" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC904" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// if nothing is connected, then remove it</span></span>
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<pre style="margin: 0;">-<span id="LC905" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">not</span> <span class="n" style="color: #333;">used</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC906" class="line" lang="cpp"> <span class="n" style="color: #333;">allowed_states</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">].</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">allowed_states</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">].</span><span class="n" style="color: #333;">begin</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">s2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC907" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC908" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC909" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC910" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">order2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">order_of_computation</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC911" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" order1 = "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">order1</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" order2 = "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">order2</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" fraction = "</span><span class="o" style="font-weight: 600;"><<</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">(</span><span class="n" style="color: #333;">order2</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">(</span><span class="n" style="color: #333;">order1</span><span class="p">)</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC912" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC913" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="cpp"><span class="n" style="color: #333;">DPmatrixConstrained</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DPmatrixConstrained</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HMM</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">M</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="cpp"> <span class="n" style="color: #333;">EmissionProbs</span><span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">d1</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="cpp"> <span class="n" style="color: #333;">EmissionProbs</span><span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">d2</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/e73664112c1ff560964d8b60a4ba295719eebc05#8361e1c55986c0d3f13504b2f7538e282eaf9893"><strong>src/mcmc/sample-alignment.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -71,16 +71,18 @@ boost::shared_ptr<DPmatrixSimple> sample_alignment_forward(data_partition P, con</td>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">state_emit</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">|=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">state_emit</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">|=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">I</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">seqlength</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">source</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">));</span> </span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">J</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">seqlength</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">source</span><span class="p">(</span><span class="n" style="color: #333;">bb</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">shared_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">DPmatrixSimple</span><span class="o" style="font-weight: 600;">></span> </span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"> <span class="n" style="color: #333;">Matrices</span><span class="p">(</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">DPmatrixSimple</span><span class="p">(</span><span class="n" style="color: #333;">HMM</span><span class="p">(</span><span class="n" style="color: #333;">state_emit</span><span class="p">,</span> <span class="n" style="color: #333;">hmm</span><span class="p">.</span><span class="n" style="color: #333;">start_pi</span><span class="p">(),</span> <span class="n" style="color: #333;">hmm</span><span class="p">,</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">get_beta</span><span class="p">()),</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">dists1</span><span class="p">),</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">dists2</span><span class="p">),</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">WeightedFrequencyMatrix</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//------------------ Compute the DP matrix ---------------------//</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// vector<vector<int> > pins= get_pins(P.alignment_constraint,A,group1,~group1,seq1,seq2);</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pins</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">yboundaries</span><span class="p">(</span><span class="n" style="color: #333;">I</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">J</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cpp"> <span class="n" style="color: #333;">Matrices</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">forward_<span class="idiff left">constrained</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">pin</span>s</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">Matrices</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">forward_<span class="idiff left">band</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">yboundarie</span>s</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Matrices</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"><span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/e73664112c1ff560964d8b60a4ba295719eebc05#17867de5076d50e87826675d7ed81840420e4676"><strong>src/meson.build</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -92,19 +92,24 @@ subdir('builtins')</td>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext">test('bali-phy version', baliphy, args:['--version'])</span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext">test('bali-phy help', baliphy, args:['--help'])</span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext">test('bali-phy 5d test', baliphy, args:[small_fasta,'--test', packagepath])</span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext">test('bali-phy 5d +A 50', baliphy, args:[small_fasta,'--iter=50', packagepath])</span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext">test('bali-phy 5d -A 200', baliphy, args:[small_fasta,'--iter=200', packagepath, '-Inone'])</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"># When running on very slow autobuilders these tests could take a long time.</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">test('bali-phy 5d +A 50', baliphy, args:[small_fasta,'--iter=50', packagepath], timeout: 180)</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">test('bali-phy 5d -A 200', baliphy, args:[small_fasta,'--iter=200', packagepath, '-Inone'], timeout:120)</span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext">#--------- Build rules for tools that are always installed ------------#</span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext">simple_tools = ['model_P','statreport','stats-select','alignment-gild','alignment-consensus', 'alignment-max','alignment-chop-internal',</span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext"> 'alignment-indices','alignment-info','alignment-cat','alignment-translate','alignment-find','trees-consensus',</span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext"> 'tree-mean-lengths','mctree-mean-lengths','trees-to-SRQ','pickout','subsample','cut-range','trees-distances', 'alignment-thin',</span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="plaintext"> 'alignments-diff'</span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="plaintext"> ]</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> 'alignments-diff','tree-tool']</span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext">foreach tool: simple_tools</span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="plaintext"> tool_exe = executable(tool, ['tools/' + tool + '.cc'], dependencies:boost, link_with: libbaliphy, install: true)</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> tool_exe = executable(tool,</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> ['tools/' + tool + '.cc'],</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> dependencies:boost,</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"> link_with: libbaliphy,</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"> install_rpath: extra_rpath,</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"> install: true)</span>
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108
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="plaintext"> test(tool + ' --help', tool_exe, args:['--help'])</span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="plaintext">endforeach</span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="plaintext"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -123,7 +128,12 @@ if get_option('extra-tools')</td>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="plaintext"> 'alignment-convert', 'alignment-find-conserved','partitions-supported','draw-graph','trees-pair-distances','tree-partitions','tree-reroot',</span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="plaintext"> 'path-graph']</span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="plaintext"> foreach tool : extra_tools</span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="plaintext"> executable( tool, ['tools/' + tool + '.cc'], dependencies: boost, link_with:libbaliphy, install:true)</span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"> executable( tool,</span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"> ['tools/' + tool + '.cc'],</span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"> dependencies: boost,</span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"> link_with:libbaliphy,</span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext"> install_rpath: extra_rpath,</span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"> install:true)</span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="plaintext"> endforeach</span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="plaintext"> all_progs = all_progs + extra_tools</span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="plaintext">endif</span>
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<li id="2a12133bc14e512e4352b8e3f5e2ad8d57e9cedc">
<a href="https://salsa.debian.org/med-team/bali-phy/commit/e73664112c1ff560964d8b60a4ba295719eebc05#2a12133bc14e512e4352b8e3f5e2ad8d57e9cedc"><strong>src/models/parameters.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -542,22 +542,19 @@ data_partition_constants::data_partition_constants(Parameters* p, int i, const a</td>
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="cpp"> <span class="n" style="color: #333;">transition_p_method_indices</span><span class="p">[</span><span class="n" style="color: #333;">b</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add_compute_expression</span><span class="p">(</span> <span class="p">{</span><span class="n" style="color: #333;">dummy</span><span class="p">(</span><span class="s" style="color: #d14;">"Prelude.!"</span><span class="p">),</span> <span class="n" style="color: #333;">transition_ps</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">}</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Add parameters for observed leaf sequence objects</span></span>
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<pre style="margin: 0;">-<span id="LC546" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">seq_counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignment_letters_counts</span><span class="p">(</span><span class="n" style="color: #333;">AA</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">n_leaves</span><span class="p">(),</span> <span class="n" style="color: #333;">counts</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">expression_ref</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">counts_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Add expressions for leaf sequences</span></span>
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">leaf_sequence_indices</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="cpp"> <span class="n" style="color: #333;">leaf_sequence_indices</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add_compute_expression</span><span class="p">(</span><span class="n" style="color: #333;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">sequences</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]));</span></span>
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="cpp"> <span class="n" style="color: #333;">counts_</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span> <span class="n" style="color: #333;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">seq_counts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC552" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Add array of leaf sequences</span></span>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">expression_ref</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seqs_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">leaf_sequence_indices</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="cpp"> <span class="n" style="color: #333;">seqs_</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_expression</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="cpp"> <span class="p">}</span></span>
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555
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">seqs_array</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_expression</span><span class="p">(</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add_compute_expression</span><span class="p">({</span><span class="n" style="color: #333;">dummy</span><span class="p">(</span><span class="s" style="color: #d14;">"Prelude.listArray'"</span><span class="p">),</span><span class="n" style="color: #333;">get_list</span><span class="p">(</span><span class="n" style="color: #333;">seqs_</span><span class="p">)})</span> <span class="p">);</span></span>
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558
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">counts_array</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_expression</span><span class="p">(</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add_compute_expression</span><span class="p">({</span><span class="n" style="color: #333;">dummy</span><span class="p">(</span><span class="s" style="color: #d14;">"Prelude.listArray'"</span><span class="p">),</span><span class="n" style="color: #333;">get_list</span><span class="p">(</span><span class="n" style="color: #333;">counts_</span><span class="p">)})</span> <span class="p">);</span></span>
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559
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="cpp"> </span>
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560
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Add methods indices for sequence lengths</span></span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Add array of pairwise alignments</span></span>
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561
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558
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">expression_ref</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">as_</span><span class="p">;</span></span>
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562
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559
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">B</span><span class="p">;</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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563
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560
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -566,6 +563,7 @@ data_partition_constants::data_partition_constants(Parameters* p, int i, const a</td>
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566
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563
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="cpp"> <span class="p">}</span></span>
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567
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564
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="cpp"> <span class="n" style="color: #333;">expression_ref</span> <span class="n" style="color: #333;">as</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_expression</span><span class="p">(</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add_compute_expression</span><span class="p">({</span><span class="n" style="color: #333;">dummy</span><span class="p">(</span><span class="s" style="color: #d14;">"Prelude.listArray'"</span><span class="p">),</span><span class="n" style="color: #333;">get_list</span><span class="p">(</span><span class="n" style="color: #333;">as_</span><span class="p">)})</span> <span class="p">);</span></span>
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568
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="cpp"></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Precompute sequence lengths</span></span>
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569
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567
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">n_nodes</span><span class="p">();</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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570
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568
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="cpp"> <span class="p">{</span></span>
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571
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569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="cpp"> <span class="n" style="color: #333;">expression_ref</span> <span class="n" style="color: #333;">L</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">dummy</span><span class="p">(</span><span class="s" style="color: #d14;">"Alignment.seqlength"</span><span class="p">),</span> <span class="n" style="color: #333;">as</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">my_tree</span><span class="p">(),</span> <span class="n" style="color: #333;">n</span><span class="p">};</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -580,6 +578,12 @@ data_partition_constants::data_partition_constants(Parameters* p, int i, const a</td>
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580
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578
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="cpp"> <span class="p">}</span></span>
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581
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579
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">likelihood_calculator</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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582
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580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="cpp"> <span class="p">{</span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">seq_counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignment_letters_counts</span><span class="p">(</span><span class="n" style="color: #333;">AA</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">n_leaves</span><span class="p">(),</span> <span class="n" style="color: #333;">counts</span><span class="p">);</span></span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">expression_ref</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">counts_</span><span class="p">;</span></span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">leaf_sequence_indices</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="cpp"> <span class="n" style="color: #333;">counts_</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span> <span class="n" style="color: #333;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">seq_counts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span> <span class="p">);</span></span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">counts_array</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_expression</span><span class="p">(</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add_compute_expression</span><span class="p">({</span><span class="n" style="color: #333;">dummy</span><span class="p">(</span><span class="s" style="color: #d14;">"Prelude.listArray'"</span><span class="p">),</span><span class="n" style="color: #333;">get_list</span><span class="p">(</span><span class="n" style="color: #333;">counts_</span><span class="p">)})</span> <span class="p">);</span></span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="cpp"></span>
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583
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587
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">my_tree</span><span class="p">();</span></span>
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584
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588
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_expression</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">PC</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">SModels</span><span class="p">[</span><span class="n" style="color: #333;">smodel_index</span><span class="p">].</span><span class="n" style="color: #333;">weighted_frequency_matrix</span><span class="p">);</span></span>
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585
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589
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="cpp"> <span class="n" style="color: #333;">cl_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add_compute_expression</span><span class="p">({</span><span class="n" style="color: #333;">dummy</span><span class="p">(</span><span class="s" style="color: #d14;">"SModel.cached_conditional_likelihoods"</span><span class="p">),</span><span class="n" style="color: #333;">t</span><span class="p">,</span><span class="n" style="color: #333;">seqs_array</span><span class="p">,</span><span class="n" style="color: #333;">counts_array</span><span class="p">,</span><span class="n" style="color: #333;">as</span><span class="p">,</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="p">,</span><span class="n" style="color: #333;">transition_ps</span><span class="p">,</span><span class="n" style="color: #333;">f</span><span class="p">});</span> <span class="c1" style="color: #998; font-style: italic;">// Create and set conditional likelihoods for each branch</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -587,6 +591,7 @@ data_partition_constants::data_partition_constants(Parameters* p, int i, const a</td>
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587
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591
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">conditional_likelihoods_for_branch</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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588
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592
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="cpp"> <span class="n" style="color: #333;">conditional_likelihoods_for_branch</span><span class="p">[</span><span class="n" style="color: #333;">b</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add_compute_expression</span><span class="p">({</span><span class="n" style="color: #333;">dummy</span><span class="p">(</span><span class="s" style="color: #d14;">"Prelude.!"</span><span class="p">),</span><span class="n" style="color: #333;">cls</span><span class="p">,</span><span class="n" style="color: #333;">b</span><span class="p">});</span></span>
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589
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593
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="cpp"></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// FIXME: broken for fixed alignments of 2 sequences.</span></span>
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590
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595
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">().</span><span class="n" style="color: #333;">n_nodes</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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591
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596
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="cpp"> <span class="p">{</span></span>
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592
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597
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="cpp"> <span class="n" style="color: #333;">expression_ref</span> <span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">dummy</span><span class="p">(</span><span class="s" style="color: #d14;">"Prelude.!"</span><span class="p">),</span> <span class="n" style="color: #333;">seqs_array</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">};</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -612,6 +617,9 @@ data_partition_constants::data_partition_constants(Parameters* p, int i, const a</td>
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612
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617
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<pre style="margin: 0;"> <span id="LC617" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">conditional_likelihoods_for_branch</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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613
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618
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<pre style="margin: 0;"> <span id="LC618" class="line" lang="cpp"> <span class="n" style="color: #333;">conditional_likelihoods_for_branch</span><span class="p">[</span><span class="n" style="color: #333;">b</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add_compute_expression</span><span class="p">({</span><span class="n" style="color: #333;">dummy</span><span class="p">(</span><span class="s" style="color: #d14;">"Prelude.!"</span><span class="p">),</span><span class="n" style="color: #333;">cls</span><span class="p">,</span><span class="n" style="color: #333;">b</span><span class="p">});</span></span>
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614
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619
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<pre style="margin: 0;"> <span id="LC619" class="line" lang="cpp"></span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="cpp"> <span class="n" style="color: #333;">object_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">Counts</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// FIXME: broken for fixed alignments of 2 sequences.</span></span>
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615
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623
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">().</span><span class="n" style="color: #333;">n_nodes</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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616
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624
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="cpp"> <span class="p">{</span></span>
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617
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625
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<pre style="margin: 0;"> <span id="LC625" class="line" lang="cpp"> <span class="n" style="color: #333;">expression_ref</span> <span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">dummy</span><span class="p">(</span><span class="s" style="color: #d14;">"Prelude.!"</span><span class="p">),</span> <span class="n" style="color: #333;">seqs_array</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">};</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -625,7 +633,7 @@ data_partition_constants::data_partition_constants(Parameters* p, int i, const a</td>
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625
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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634
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="cpp"> <span class="p">{</span></span>
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627
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635
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">root</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parameter</span><span class="p">(</span><span class="s" style="color: #d14;">"*subst_root"</span><span class="p">);</span></span>
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628
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<pre style="margin: 0;">-<span id="LC628" class="line" lang="cpp"> <span class="n" style="color: #333;">likelihood_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add_compute_expression</span><span class="p">({</span><span class="n" style="color: #333;">dummy</span><span class="p">(</span><span class="s" style="color: #d14;">"SModel.peel_likelihood_SEV"</span><span class="p">),</span> <span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">root</span><span class="p">});</span></span>
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="cpp"> <span class="n" style="color: #333;">likelihood_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add_compute_expression</span><span class="p">({</span><span class="n" style="color: #333;">dummy</span><span class="p">(</span><span class="s" style="color: #d14;">"SModel.peel_likelihood_SEV"</span><span class="p">),</span> <span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">root</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">Counts</span></span><span class="p">});</span></span>
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629
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="cpp"> <span class="p">}</span></span>
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638
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="cpp"> <span class="p">}</span></span>
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639
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/e73664112c1ff560964d8b60a4ba295719eebc05#793e98e2860c5009cc477e9a83aeadbab0aa9081"><strong>src/startup/A-T-model.H</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -36,7 +36,7 @@ owned_ptr<Model> create_A_and_T_model(const Rules& R, boost::program_options::va</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">out_cache</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">out_screen</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">out_both</span><span class="p">,</span> <span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">info</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">proc_id</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">write_initial_alignments</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">owned_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">Model</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">M</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">proc_id</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">string</span></span> <span class="n" style="color: #333;">dir_name</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">write_initial_alignments</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">boost</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">program_options</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">variables_map</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">proc_id</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">&</span></span> <span class="n" style="color: #333;">dir_name</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/e73664112c1ff560964d8b60a4ba295719eebc05#d58858ee516bfdb1c86c6b43708b0bdc4329e15b"><strong>src/startup/A-T-model.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,6 +11,9 @@</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "startup/help.hh"</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "computation/expression/lambda.H"</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/optional/optional_io.hpp></span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/filesystem/operations.hpp></span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">fs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">po</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">po</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variables_map</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -651,14 +654,14 @@ owned_ptr<Model> create_A_and_T_model(const Rules& R, variables_map& args, const</td>
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651
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654
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<pre style="margin: 0;"> <span id="LC654" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">likelihood_calculators</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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655
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<pre style="margin: 0;"> <span id="LC655" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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653
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656
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">myexception</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"Calculator "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" not recognized!"</span><span class="p">;</span></span>
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654
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<pre style="margin: 0;">-<span id="LC654" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">imodel_mapping</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">)</span></span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">imodel_mapping</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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655
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658
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">myexception</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"Calculator "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" does not work with a variable alignment!"</span><span class="p">;</span></span>
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656
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659
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<pre style="margin: 0;"> <span id="LC659" class="line" lang="cpp"> <span class="p">}</span></span>
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657
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660
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="cpp"> <span class="p">}</span></span>
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658
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661
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="cpp"></span>
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659
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662
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">unalign</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"unalign"</span><span class="p">);</span></span>
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660
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663
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<pre style="margin: 0;"> <span id="LC663" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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661
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unalign</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">imodel_mapping</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">)</span></span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unalign</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">imodel_mapping</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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662
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665
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">likelihood_calculators</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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663
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666
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">myexception</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"Can't unalign with calculator "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">likelihood_calculators</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"!"</span><span class="p">;</span></span>
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667
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="cpp"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -711,22 +714,21 @@ owned_ptr<Model> create_A_and_T_model(const Rules& R, variables_map& args, const</td>
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711
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714
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<pre style="margin: 0;"> <span id="LC714" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">P</span><span class="p">;</span></span>
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712
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715
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<pre style="margin: 0;"> <span id="LC715" class="line" lang="cpp"><span class="p">}</span></span>
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713
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716
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC714" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">write_initial_alignments</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">owned_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">Model</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">M</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">proc_id</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">string</span></span> <span class="n" style="color: #333;">dir_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">write_initial_alignments</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">variables_map</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">proc_id</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">&</span></span> <span class="n" style="color: #333;">dir_name</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC716" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Parameters</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">M</span><span class="p">.</span><span class="n" style="color: #333;">as</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Parameters</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>
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717
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<pre style="margin: 0;">-<span id="LC717" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">not</span> <span class="n" style="color: #333;">P</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">filenames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="s" style="color: #d14;">"align"</span><span class="p">].</span><span class="n" style="color: #333;">as</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>
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720
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC719" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">P</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">().</span></span><span class="n" style="color: #333;"><span class="idiff">n_nodes</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">return</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">fs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dir</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">dir_name</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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722
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC721" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">alignment</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">A</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC722" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">P</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_data_partitions</span><span class="p">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC723" class="line" lang="cpp"> <span class="n" style="color: #333;">A</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">P</span><span class="p">)[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">A</span><span class="p">());</span></span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"C"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">convertToString</span><span class="p">(</span><span class="n" style="color: #333;">proc_id</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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724
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<pre style="margin: 0;"> <span id="LC724" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC725" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">string</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">base</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dir_name</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"/"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"C"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">convertToString</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">proc_id</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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<pre style="margin: 0;">-<span id="LC726" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">A</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">();</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">++</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span></span>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">auto</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">filenames</span></span><span class="p">)</span></span>
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727
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC728" class="line" lang="cpp"> <span class="n" style="color: #333;">checked_ofstream</span> <span class="n" style="color: #333;">file</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".P"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">convertToString</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".initial.fasta"</span><span class="p">);</span></span>
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729
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<pre style="margin: 0;">-<span id="LC729" class="line" lang="cpp"> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">A</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">source</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fs</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">target</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fs</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".P"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">convertToString</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".initial.fasta"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="cpp"> <span class="n" style="color: #333;">fs</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">copy_file</span><span class="p">(</span><span class="n" style="color: #333;">source</span><span class="p">,</span><span class="n" style="color: #333;">dir</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">target</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC732" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC733" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC734" class="line" lang="cpp"></span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -308,7 +308,7 @@ optional<string> get_citation(const Rule& rule, bool show_title)</td>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="cpp"><span class="n" style="color: #333;">optional</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">get_citation_<span class="idiff left">doi</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Rule</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">rul</span>e</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp"><span class="n" style="color: #333;">optional</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">get_citation_<span class="idiff left">id</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Rule</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rule</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">idtyp</span>e</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="cpp"><span class="p">{</span></span>
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313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 1. Check if there is a citation field.</span></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">citation</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rule</span><span class="p">.</span><span class="n" style="color: #333;">get_child_optional</span><span class="p">(</span><span class="s" style="color: #d14;">"citation"</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -320,7 +320,7 @@ optional<string> get_citation_doi(const Rule& rule)</td>
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">identifier</span><span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">identifiers</span><span class="p">)</span></span>
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321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="cpp"> <span class="p">{</span></span>
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322
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322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">identifier</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">get_child_optional</span><span class="p">(</span><span class="s" style="color: #d14;">"type"</span><span class="p">);</span></span>
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323
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">not</span> <span class="n" style="color: #333;">type</span> <span class="n" style="color: #333;">or</span> <span class="n" style="color: #333;">type</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_value</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;"><span class="idiff left right">"doi"</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">not</span> <span class="n" style="color: #333;">type</span> <span class="n" style="color: #333;">or</span> <span class="n" style="color: #333;">type</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_value</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;"><span class="idiff left right">idtype</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">identifier</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">get_child_optional</span><span class="p">(</span><span class="s" style="color: #d14;">"id"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">id</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -353,10 +353,18 @@ optional<string> get_citation_url(const Rule& rule)</td>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="cpp"> <span class="p">}</span></span>
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355
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">doi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_citation_<span class="idiff left">doi</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">rule</span></span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">doi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_citation_<span class="idiff left">id</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">rule</span></span><span class="p"><span class="idiff">,</span></span><span class="s" style="color: #d14;"><span class="idiff right">"doi"</span></span><span class="p">))</span></span>
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357
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"https://doi.org/"</span><span class="o" style="font-weight: 600;">+*</span><span class="n" style="color: #333;">doi</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">pmcid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_citation_id</span><span class="p">(</span><span class="n" style="color: #333;">rule</span><span class="p">,</span><span class="s" style="color: #d14;">"pmcid"</span><span class="p">))</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="cpp"> <span class="p">{</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"https://www.ncbi.nlm.nih.gov/pmc/articles/"</span><span class="o" style="font-weight: 600;">+*</span><span class="n" style="color: #333;">pmcid</span><span class="p">;</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">pmid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_citation_id</span><span class="p">(</span><span class="n" style="color: #333;">rule</span><span class="p">,</span><span class="s" style="color: #d14;">"pmid"</span><span class="p">))</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cpp"> <span class="p">{</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"https://www.ncbi.nlm.nih.gov/pubmed/"</span><span class="o" style="font-weight: 600;">+*</span><span class="n" style="color: #333;">pmid</span><span class="p">;</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cpp"> <span class="p">}</span></span>
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360
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368
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="cpp"></span>
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361
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">none</span><span class="p">;</span></span>
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362
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -390,7 +398,8 @@ string get_help_for_rule(const Rules& rules, const Rule& rule)</td>
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390
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="cpp"> <span class="p">}</span></span>
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391
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="cpp"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">header</span><span class="p">(</span><span class="s" style="color: #d14;">"Usage"</span><span class="p">);</span></span>
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392
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400
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="cpp"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">bold</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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393
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<td class="diff-line-num new_line old" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args_names_types</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"["</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">args_names_types</span><span class="p">,</span><span class="s" style="color: #d14;">", "</span><span class="p">)</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"]</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args_names_types</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"["</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">args_names_types</span><span class="p">,</span><span class="s" style="color: #d14;">", "</span><span class="p">)</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"]"</span><span class="p">;</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="cpp"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
394
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<td class="diff-line-num new_line" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="cpp"> </span>
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<td class="diff-line-num old_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
395
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<td class="diff-line-num new_line" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
404
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">synonyms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rule</span><span class="p">.</span><span class="n" style="color: #333;">get_child_optional</span><span class="p">(</span><span class="s" style="color: #d14;">"synonyms"</span><span class="p">))</span></span>
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<td class="diff-line-num old_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
396
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<td class="diff-line-num new_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -401,7 +410,8 @@ string get_help_for_rule(const Rules& rules, const Rule& rule)</td>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="cpp"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">header</span><span class="p">(</span><span class="s" style="color: #d14;">"Arguments"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">not</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="cpp"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">header</span><span class="p">(</span><span class="s" style="color: #d14;">"Arguments"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">argpair</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argpair</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/e73664112c1ff560964d8b60a4ba295719eebc05#b08039b44d681fdea6e22ae2712d6e01307dad0a"><strong>src/substitution/substitution.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -527,7 +527,8 @@ namespace substitution {</td>
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="cpp"> <span class="n" style="color: #333;">log_double_t</span> <span class="n" style="color: #333;">calc_root_probability_SEV</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Likelihood_Cache_Branch</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">LCB1</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Likelihood_Cache_Branch</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">LCB2</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Likelihood_Cache_Branch</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">LCB3</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Matrix</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">F</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Matrix</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">F</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">counts</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="cpp"> <span class="n" style="color: #333;">total_calc_root_prob</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -557,6 +558,7 @@ namespace substitution {</td>
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">L</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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558
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559
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">L</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bits2</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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559
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560
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">L</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bits3</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">L</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">counts</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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560
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562
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="cpp"></span>
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561
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563
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="cpp"> <span class="n" style="color: #333;">total_root_clv_length</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">L</span><span class="p">;</span></span>
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562
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564
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -630,7 +632,7 @@ namespace substitution {</td>
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632
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">non_gap2</span><span class="p">)</span> <span class="n" style="color: #333;">i2</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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631
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633
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">non_gap3</span><span class="p">)</span> <span class="n" style="color: #333;">i3</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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634
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC633" class="line" lang="cpp"> <span class="n" style="color: #333;">total</span><span class="p">.</span><span class="n" style="color: #333;">mult_with_count</span><span class="p">(</span><span class="n" style="color: #333;">p_col</span><span class="p">,</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="cpp"> <span class="n" style="color: #333;">total</span><span class="p">.</span><span class="n" style="color: #333;">mult_with_count</span><span class="p">(</span><span class="n" style="color: #333;">p_col</span><span class="p">,</span><span class="n" style="color: #333;"><span class="idiff left">counts</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">c</span></span><span class="p"><span class="idiff right">]</span>);</span></span>
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// std::clog<<" i = "<<i<<" p = "<<p_col<<" total = "<<total<<"\n";</span></span>
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637
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/e73664112c1ff560964d8b60a4ba295719eebc05#66d5dbdd0848e5daf8dd55d33e87059e24b62551"><strong>src/tools/alignment-draw.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -184,6 +184,8 @@ public:</td>
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="cpp"> <span class="p">{</span></span>
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185
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">white</span><span class="p">;</span></span>
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186
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="cpp"></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">n_blocks</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">HSV</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"> </span>
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187
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="cpp"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">n_blocks</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// otherwise use the rainbow</span></span>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/e73664112c1ff560964d8b60a4ba295719eebc05#c71ed633fd98d76cd79b35c4870d0093fbf370bd"><strong>src/tools/alignments-diff.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -89,7 +89,7 @@ variables_map parse_cmd_line(int argc,char* argv[])</td>
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89
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"fill"</span><span class="p">,</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="s" style="color: #d14;">"gap"</span><span class="p">),</span><span class="s" style="color: #d14;">"blank columns filled with: gap or unknown"</span><span class="p">)</span></span>
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90
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"differences-file,d"</span><span class="p">,</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">(),</span><span class="s" style="color: #d14;">"Filename to store differences in AU format"</span><span class="p">)</span></span>
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91
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"blocksize"</span><span class="p">,</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="p">),</span><span class="s" style="color: #d14;">"Width of blocks of same color"</span><span class="p">)</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"classes"</span><span class="p">,</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">3</span></span><span class="p">),</span><span class="s" style="color: #d14;">"Number of groups for non-matching characters"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"classes"</span><span class="p">,</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">),</span><span class="s" style="color: #d14;">"Number of groups for non-matching characters"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"> <span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">options_description</span> <span class="n" style="color: #333;">all</span><span class="p">(</span><span class="s" style="color: #d14;">"All options"</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/e73664112c1ff560964d8b60a4ba295719eebc05#84999b84377c68efe88974cfb9b4180e6d617841"><strong>src/tools/tree-tool.cc</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> Copyright (C) 2005-2009 Benjamin Redelings</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> This file is part of BAli-Phy.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> BAli-Phy is free software; you can redistribute it and/or modify it under</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> the terms of the GNU General Public License as published by the Free</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> Software Foundation; either version 2, or (at your option) any later</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> version.</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> BAli-Phy is distributed in the hope that it will be useful, but WITHOUT ANY</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> WARRANTY; without even the implied warranty of MERCHANTABILITY or</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for more details.</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> You should have received a copy of the GNU General Public License</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> along with BAli-Phy; see the file COPYING. If not see</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> <http://www.gnu.org/licenses/>. */</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <list></span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <utility></span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "tree/tree.H"</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "tree/sequencetree.H"</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "tree/tree-util.H"</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "tree-dist.H"</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "myexception.H"</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "util/assert.hh"</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/program_options.hpp></span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">dynamic_bitset</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">po</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">po</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variables_map</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">list</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">valarray</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">optional</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"><span class="n" style="color: #333;">variables_map</span> <span class="nf" style="color: #900; font-weight: 600;">parse_cmd_line</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[])</span> </span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"><span class="p">{</span> </span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">po</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// named options</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"> <span class="n" style="color: #333;">options_description</span> <span class="n" style="color: #333;">invisible</span><span class="p">(</span><span class="s" style="color: #d14;">"Invisible options"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"> <span class="n" style="color: #333;">invisible</span><span class="p">.</span><span class="n" style="color: #333;">add_options</span><span class="p">()</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"tree"</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">(),</span><span class="s" style="color: #d14;">"tree to operate on"</span><span class="p">);</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"> <span class="n" style="color: #333;">options_description</span> <span class="n" style="color: #333;">general</span><span class="p">(</span><span class="s" style="color: #d14;">"General options"</span><span class="p">);</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">general</span><span class="p">.</span><span class="n" style="color: #333;">add_options</span><span class="p">()</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"help,h"</span><span class="p">,</span> <span class="s" style="color: #d14;">"produce help message"</span><span class="p">)</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"verbose,v"</span><span class="p">,</span><span class="s" style="color: #d14;">"Output more log messages on stderr."</span><span class="p">)</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"> <span class="p">;</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">options_description</span> <span class="n" style="color: #333;">commands</span><span class="p">(</span><span class="s" style="color: #d14;">"Commands"</span><span class="p">);</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"> <span class="n" style="color: #333;">commands</span><span class="p">.</span><span class="n" style="color: #333;">add_options</span><span class="p">()</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"prune"</span><span class="p">,</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">(),</span><span class="s" style="color: #d14;">"Comma-separated taxa to remove"</span><span class="p">)</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"resolve"</span><span class="p">,</span><span class="s" style="color: #d14;">"Comma-separated taxa to remove"</span><span class="p">)</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="p">;</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">options_description</span> <span class="n" style="color: #333;">visible</span><span class="p">(</span><span class="s" style="color: #d14;">"All options"</span><span class="p">);</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="n" style="color: #333;">visible</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">general</span><span class="p">).</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">commands</span><span class="p">);</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">options_description</span> <span class="n" style="color: #333;">all</span><span class="p">(</span><span class="s" style="color: #d14;">"All options"</span><span class="p">);</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">all</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">general</span><span class="p">).</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">commands</span><span class="p">).</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">invisible</span><span class="p">);</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// positional options</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;">positional_options_description</span> <span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="s" style="color: #d14;">"tree"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> </span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <span class="n" style="color: #333;">variables_map</span> <span class="n" style="color: #333;">args</span><span class="p">;</span> </span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="n" style="color: #333;">store</span><span class="p">(</span><span class="n" style="color: #333;">command_line_parser</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">).</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="n" style="color: #333;">options</span><span class="p">(</span><span class="n" style="color: #333;">all</span><span class="p">).</span><span class="n" style="color: #333;">positional</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">).</span><span class="n" style="color: #333;">run</span><span class="p">(),</span> <span class="n" style="color: #333;">args</span><span class="p">);</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">notify</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">);</span> </span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"help"</span><span class="p">))</span> <span class="p">{</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"Perform various operations on Newick trees.</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"Usage: tree-tool <tree-file> [OPTIONS]</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">general</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">commands</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="p">}</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"verbose"</span><span class="p">))</span> <span class="n" style="color: #333;">log_verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">args</span><span class="p">;</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"><span class="p">}</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">resolve</span><span class="p">(</span><span class="n" style="color: #333;">Tree</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">T</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">node</span><span class="p">)</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"><span class="p">{</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">)</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="p">{</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">neighbors</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">neighbors</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">);</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">neighbors</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">new_node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">create_node_on_branch</span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">directed_branch</span><span class="p">(</span><span class="n" style="color: #333;">neighbors</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">node</span><span class="p">)).</span><span class="n" style="color: #333;">name</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">not</span> <span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">directed_branch</span><span class="p">(</span><span class="n" style="color: #333;">new_node</span><span class="p">,</span><span class="n" style="color: #333;">node</span><span class="p">).</span><span class="n" style="color: #333;">has_length</span><span class="p">())</span></span>
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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">directed_branch</span><span class="p">(</span><span class="n" style="color: #333;">new_node</span><span class="p">,</span><span class="n" style="color: #333;">node</span><span class="p">).</span><span class="n" style="color: #333;">set_length</span><span class="p">(</span><span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">not</span> <span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">directed_branch</span><span class="p">(</span><span class="n" style="color: #333;">new_node</span><span class="p">,</span><span class="n" style="color: #333;">neighbors</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]).</span><span class="n" style="color: #333;">has_length</span><span class="p">())</span></span>
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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">directed_branch</span><span class="p">(</span><span class="n" style="color: #333;">new_node</span><span class="p">,</span><span class="n" style="color: #333;">neighbors</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]).</span><span class="n" style="color: #333;">set_length</span><span class="p">(</span><span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> </span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">reconnect_branch</span><span class="p">(</span><span class="n" style="color: #333;">neighbors</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="n" style="color: #333;">node</span><span class="p">,</span><span class="n" style="color: #333;">new_node</span><span class="p">);</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">node</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">).</span><span class="n" style="color: #333;">degree</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">neighbors</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="p">}</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"><span class="p">}</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">polytomies</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Tree</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">T</span><span class="p">)</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"><span class="p">{</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">n_nodes</span><span class="p">();</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">node</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">).</span><span class="n" style="color: #333;">degree</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[])</span> </span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"><span class="p">{</span> </span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//----------- Parse command line ----------//</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">variables_map</span> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_cmd_line</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span><span class="n" style="color: #333;">argv</span><span class="p">);</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">prune</span><span class="p">;</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"prune"</span><span class="p">))</span> <span class="p">{</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="s" style="color: #d14;">"prune"</span><span class="p">].</span><span class="n" style="color: #333;">as</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="n" style="color: #333;">prune</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span><span class="sc" style="color: #d14;">','</span><span class="p">);</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//----------- Read the topology -----------//</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">SequenceTree</span> <span class="n" style="color: #333;">T</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">load_T</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">);</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"resolve"</span><span class="p">))</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="p">{</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">polytomies</span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"> <span class="n" style="color: #333;">resolve</span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">,</span><span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">polytomies</span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">).</span><span class="n" style="color: #333;">empty</span><span class="p">());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"tree-tool: Error! "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">what</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"><span class="p">}</span></span></pre>
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