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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/6d3ce2e54b62bdc0e1b80911d4bdb27a5b6f5260">6d3ce2e5</a></strong>
<div>
<span>by Benjamin Redelings</span>
<i>at 2018-05-05T08:01:56-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.1.1+dfsg</pre>
</li>
</ul>
<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#c2eebab294e65ea30942617fec043f1a3e237a39">
functions/gtr.json
</a>
</li>
<li class="file-stats">
<a href="#1be21e121b4d836a5e47d11df3711050378cbcdb">
functions/hky85.json
</a>
</li>
<li class="file-stats">
<a href="#0a90a7ef83788387ced3bf79917dab91682900a4">
functions/tn93.json
</a>
</li>
<li class="file-stats">
<a href="#0cc1139e3347f573ae1feee5b73dbc8a8a21fcfa">
meson.build
</a>
</li>
<li class="file-stats">
<a href="#cee142ff88dc5968288cf8e6adf24f1cf67facdf">
src/models/rules.cc
</a>
</li>
<li class="file-stats">
<a href="#73597fa753595b2d338c9cff09963f945b6b18db">
src/models/setup.H
</a>
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<li class="file-stats">
<a href="#94c1320ff59df5a7dbd1f999929b578c570fd365">
src/models/setup.cc
</a>
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<li class="file-stats">
<a href="#d58858ee516bfdb1c86c6b43708b0bdc4329e15b">
src/startup/A-T-model.cc
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="c2eebab294e65ea30942617fec043f1a3e237a39">
<a href="https://salsa.debian.org/med-team/bali-phy/commit/6d3ce2e54b62bdc0e1b80911d4bdb27a5b6f5260#c2eebab294e65ea30942617fec043f1a3e237a39"><strong>functions/gtr.json</strong></a>
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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="json"><span class="p">{</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="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;">"gtr"</span><span class="p">,</span></span>
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3
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
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<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="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"title"</span><span class="p">:</span><span class="s2" style="color: #d14;">"The GTR exchangability matrix"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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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="LC4" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"deprecated-synonyms"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;">"GTR"</span><span class="p">],</span></span>
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4
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" 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;">"RevCTMC[a]"</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" 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.gtr'[sym,pi,a]"</span><span class="p">,</span></span>
</pre>
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6
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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;">"citation"</span><span class="p">:</span><span class="s2" style="color: #d14;">"Tavare, 1986"</span><span class="p">,</span></span>
</pre>
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<li id="1be21e121b4d836a5e47d11df3711050378cbcdb">
<a href="https://salsa.debian.org/med-team/bali-phy/commit/6d3ce2e54b62bdc0e1b80911d4bdb27a5b6f5260#1be21e121b4d836a5e47d11df3711050378cbcdb"><strong>functions/hky85.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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<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;">"hky85"</span><span class="p">,</span></span>
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
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<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="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 Hasegawa-Kishino-Yano (1985) nucleotide rate matrix"</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;">"deprecated-synonyms"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;">"HKY"</span><span class="p">,</span><span class="s2" style="color: #d14;">"hky"</span><span class="p">,</span><span class="s2" style="color: #d14;">"HKY85"</span><span class="p">],</span></span>
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4
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" 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;">"RevCTMC[a]"</span><span class="p">,</span></span>
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5
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"constraints"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;">"Nucleotides[a]"</span><span class="p">],</span></span>
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6
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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;">"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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<a href="https://salsa.debian.org/med-team/bali-phy/commit/6d3ce2e54b62bdc0e1b80911d4bdb27a5b6f5260#0a90a7ef83788387ced3bf79917dab91682900a4"><strong>functions/tn93.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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<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;">"tn93"</span><span class="p">,</span></span>
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3
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3
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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="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 Tamura-Nei (1993) nucleotide rate matrix"</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;">"deprecated-synonyms"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;">"TN"</span><span class="p">,</span><span class="s2" style="color: #d14;">"TrN"</span><span class="p">,</span><span class="s2" style="color: #d14;">"tn"</span><span class="p">,</span><span class="s2" style="color: #d14;">"TN93"</span><span class="p">,</span><span class="s2" style="color: #d14;">"trn"</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;">"result_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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<pre style="margin: 0;"> <span id="LC6" 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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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;">"title"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees."</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/6d3ce2e54b62bdc0e1b80911d4bdb27a5b6f5260#0cc1139e3347f573ae1feee5b73dbc8a8a21fcfa"><strong>meson.build</strong></a>
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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>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> version: '3.1<span class="idiff left right">.1</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">@@ -130,14 +130,23 @@ subdir('src')</td>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="plaintext">subdir('doc')</span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"># Run internal tests</span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">run_tests = find_program(join_paths(meson.source_root(),'tests/run-tests.py'))</span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="plaintext">test('bali-phy testsuite',</span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="plaintext"> <span class="idiff left right">find_program('tests/run-tests.py')</span>,</span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"> <span class="idiff left right">run_tests</span>,</span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="plaintext"> timeout: 600,</span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="plaintext"> workdir: join_paths(meson.source_root(),'tests'),</span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="plaintext"> args:[baliphy.full_path(), packagepath])</span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="plaintext">test('testiphy (likelihood testsuite)',</span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="plaintext"> find_program('testiphy/testiphy'),</span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="plaintext"> timeout: 600,</span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="plaintext"> workdir: join_paths(meson.source_root(),'testiphy'),</span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="plaintext"> args:[baliphy.full_path(), packagepath])</span></pre>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"># Run external likelihood testsuite</span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">testiphy = find_program(join_paths(meson.source_root(),'testiphy/testiphy'), required: false)</span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">if testiphy.found()</span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext"> test('testiphy (likelihood testsuite)',</span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext"> testiphy,</span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext"> timeout: 600,</span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"> workdir: join_paths(meson.source_root(),'testiphy'),</span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"> args:[baliphy.full_path(), packagepath])</span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">endif</span></pre>
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<li id="cee142ff88dc5968288cf8e6adf24f1cf67facdf">
<a href="https://salsa.debian.org/med-team/bali-phy/commit/6d3ce2e54b62bdc0e1b80911d4bdb27a5b6f5260#cee142ff88dc5968288cf8e6adf24f1cf67facdf"><strong>src/models/rules.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">@@ -190,7 +190,7 @@ optional<Rule> Rules::get_rule_for_func(const string& s) const</td>
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190
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<pre style="margin: 0;"> <span id="LC190" 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;">syn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">get_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="p">(</span><span class="s" style="color: #d14;">"synonym"</span><span class="p">))</span></span>
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">get_rule_for_func</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">syn</span><span class="p">);</span></span>
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192
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192
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<pre style="margin: 0;"> <span id="LC192" 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;">syn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">get_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="p">(</span><span class="s" style="color: #d14;">"deprecated-synonym"</span><span class="p">))</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" 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;">"<span class="idiff left">Error: the function '"</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="n" style="color: #333;"><span class="idiff">s</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="s" style="color: #d14;"><span class="idiff">"' is now called '"</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><<*</span></span><span class="n" style="color: #333;"><span class="idiff">syn</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="s" style="color: #d14;"><span class="idiff right">"'</span>"</span><span class="p">;</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" 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;">"<span class="idiff left">I don't recognize '"</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="n" style="color: #333;"><span class="idiff">s</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="s" style="color: #d14;"><span class="idiff">"'. Perhaps you meant '"</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><<*</span></span><span class="n" style="color: #333;"><span class="idiff">syn</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="s" style="color: #d14;"><span class="idiff right">"'?</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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196
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cpp"><span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/6d3ce2e54b62bdc0e1b80911d4bdb27a5b6f5260#73597fa753595b2d338c9cff09963f945b6b18db"><strong>src/models/setup.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">@@ -23,6 +23,8 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC23" 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;">pretty_model_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">terms</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC25" 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;">string</span> <span class="n" style="color: #333;">show</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Rules</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">R</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</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="LC26" 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;">string</span> <span class="n" style="color: #333;">show_main</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Rules</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</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="LC27" 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;">string</span> <span class="n" style="color: #333;">show_extracted</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Rules</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>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"> <span class="n" style="color: #333;">pretty_model_t</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ptree</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="LC30" class="line" lang="c"><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">@@ -40,6 +42,8 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC42" 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;">string</span> <span class="n" style="color: #333;">show</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Rules</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</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="LC43" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC44" 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;">string</span> <span class="n" style="color: #333;">show_pretty</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Rules</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</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="LC45" 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;">string</span> <span class="n" style="color: #333;">show_main</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Rules</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</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="LC46" 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;">string</span> <span class="n" style="color: #333;">show_extracted</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Rules</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>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"> <span class="n" style="color: #333;">model_t</span><span class="p">()</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">default</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"> <span class="n" style="color: #333;">model_t</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ptree</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;">ptree</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;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">term_t</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;">expression_ref</span><span class="o" style="font-weight: 600;">&</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/6d3ce2e54b62bdc0e1b80911d4bdb27a5b6f5260#94c1320ff59df5a7dbd1f999929b578c570fd365"><strong>src/models/setup.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">@@ -118,6 +118,18 @@ string model_t::show_pretty(const Rules& rules, bool top) const</td>
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">show</span><span class="p">(</span><span class="n" style="color: #333;">rules</span><span class="p">,</span> <span class="n" style="color: #333;">not</span> <span class="n" style="color: #333;">top</span><span class="p">);</span></span>
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"><span class="p">}</span></span>
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120
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">model_t</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">show_main</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Rules</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rules</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">top</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="LC122" 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="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pretty_model_t</span><span class="p">(</span><span class="n" style="color: #333;">description</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">show_main</span><span class="p">(</span><span class="n" style="color: #333;">rules</span><span class="p">,</span> <span class="n" style="color: #333;">top</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">model_t</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">show_extracted</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Rules</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rules</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pretty_model_t</span><span class="p">(</span><span class="n" style="color: #333;">description</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">show_extracted</span><span class="p">(</span><span class="n" style="color: #333;">rules</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"><span class="n" style="color: #333;">model_t</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">model_t</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ptree</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ptree</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">t</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;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">term_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">c</span><span class="p">,</span> <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;">e</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">description</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">),</span> <span class="n" style="color: #333;">type</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">),</span> <span class="n" style="color: #333;">constraints</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">),</span> <span class="n" style="color: #333;">expression</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC135" 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">@@ -649,15 +661,11 @@ vector<pair<string, ptree>> extract_terms(ptree& m)</td>
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC662" 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="LC663" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC652" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">pretty_model_t</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">show</span><span class="p"><span class="idiff left">(</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">Rules</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">R</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">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">top</span></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="LC664" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">pretty_model_t</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">show<span class="idiff left">_extracted</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">Rules</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">R</span></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="LC665" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC666" 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;">indent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">output</span><span class="p">;</span></span>
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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;">top</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC658" class="line" lang="cpp"> <span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unparse</span><span class="p">(</span><span class="n" style="color: #333;">extract_value</span><span class="p">(</span><span class="n" style="color: #333;">main</span><span class="p">),</span> <span class="n" style="color: #333;">R</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC659" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC660" class="line" lang="cpp"> <span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">show_model</span><span class="p">(</span><span class="n" style="color: #333;">extract_value</span><span class="p">(</span><span class="n" style="color: #333;">main</span><span class="p">),</span> <span class="n" style="color: #333;">R</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC670" 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;">terms</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="LC671" 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">@@ -668,6 +676,19 @@ string pretty_model_t::show(const Rules& R, bool top) const</td>
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">output</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">pretty_model_t</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">show_main</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Rules</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">R</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">top</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="LC680" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">top</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">unparse</span><span class="p">(</span><span class="n" style="color: #333;">extract_value</span><span class="p">(</span><span class="n" style="color: #333;">main</span><span class="p">),</span> <span class="n" style="color: #333;">R</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">show_model</span><span class="p">(</span><span class="n" style="color: #333;">extract_value</span><span class="p">(</span><span class="n" style="color: #333;">main</span><span class="p">),</span> <span class="n" style="color: #333;">R</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">pretty_model_t</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">show</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Rules</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">R</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">top</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="LC688" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">show_main</span><span class="p">(</span><span class="n" style="color: #333;">R</span><span class="p">,</span><span class="n" style="color: #333;">top</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">show_extracted</span><span class="p">(</span><span class="n" style="color: #333;">R</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="cpp"><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;">pretty_model_t</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pretty_model_t</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ptree</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="LC693" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">main</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC694" class="line" lang="cpp"><span class="p">{</span></span>
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<li id="d58858ee516bfdb1c86c6b43708b0bdc4329e15b">
<a href="https://salsa.debian.org/med-team/bali-phy/commit/6d3ce2e54b62bdc0e1b80911d4bdb27a5b6f5260#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">@@ -142,6 +142,13 @@ json optional_to_json(const boost::optional<T>& o)</td>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">o</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// FIXME - maybe we should try to make a single giant model so that we get S1/parameter</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// exactly when this occurs for the logged parameter names, themselves.</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// This would also help it we have some variables that are outside of models, because</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// they are shared between them.</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"></span>
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145
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"><span class="n" style="color: #333;">json</span> <span class="n" style="color: #333;">log_summary</span><span class="p">(</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;">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;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">out_both</span><span class="p">,</span></span>
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146
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153
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<pre style="margin: 0;"> <span id="LC153" 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="n" style="color: #333;">model_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">IModels</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;">model_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">SModels</span><span class="p">,</span></span>
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147
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154
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<pre style="margin: 0;"> <span id="LC154" 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="n" style="color: #333;">model_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">ScaleModels</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">@@ -151,30 +158,61 @@ json log_summary(ostream& out_cache, ostream& out_screen,ostream& out_both,</td>
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151
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"> <span class="n" style="color: #333;">json</span> <span class="n" style="color: #333;">info</span><span class="p">;</span></span>
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152
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp"> <span class="n" style="color: #333;">json</span> <span class="n" style="color: #333;">partitions</span><span class="p">;</span></span>
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153
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp"></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"> <span class="n" style="color: #333;">json</span> <span class="n" style="color: #333;">tree</span><span class="p">;</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" 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="p">.</span><span class="n" style="color: #333;">t</span><span class="p">().</span><span class="n" style="color: #333;">n_branches</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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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"> <span class="p">{</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"> <span class="n" style="color: #333;">out_both</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"T:topology ~ uniform on tree topologies</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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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"> <span class="n" style="color: #333;">tree</span><span class="p">[</span><span class="s" style="color: #d14;">"topology"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"uniform"</span><span class="p">;</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"> <span class="p">}</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"></span>
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168
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<pre style="margin: 0;">+<span id="LC168" 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="p">.</span><span class="n" style="color: #333;">t</span><span class="p">().</span><span class="n" style="color: #333;">n_branches</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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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="p">{</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"> <span class="n" style="color: #333;">out_both</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"T:lengths "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">branch_length_model</span><span class="p">.</span><span class="n" style="color: #333;">show</span><span class="p">(</span><span class="n" style="color: #333;">rules</span><span class="p">)</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</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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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"> <span class="n" style="color: #333;">tree</span><span class="p">[</span><span class="s" style="color: #d14;">"lengths"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">branch_length_model</span><span class="p">.</span><span class="n" style="color: #333;">show</span><span class="p">(</span><span class="n" style="color: #333;">rules</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp"> <span class="p">}</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"></span>
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154
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//-------- Log some stuff -----------//</span></span>
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155
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<td class="diff-line-num new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
175
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<pre style="margin: 0;"> <span id="LC175" 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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156
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="cpp"></span>
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157
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<td class="diff-line-num new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
177
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<pre style="margin: 0;"> <span id="LC177" 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="p">.</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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158
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="cpp"> <span class="p">{</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" 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">a_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="n" style="color: #333;"><span class="idiff">P</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">get_alphabet</span></span><span class="p"><span class="idiff">().</span></span><span class="n" style="color: #333;"><span class="idiff right">name</span></span><span class="p">;</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">json</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">partition</span></span><span class="p">;</span></span>
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160
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="161" 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">
161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="cpp"> <span class="n" style="color: #333;">out_cache</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"data"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="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;">filenames</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="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 old old_line" data-linenumber="162" 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">
162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">out_cache</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"alphabet"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="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;">a_name</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</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 old old_line" data-linenumber="163" 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">
163
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<td class="diff-line-num new_line old" data-linenumber="181" 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="LC163" class="line" lang="cpp"> <span class="n" style="color: #333;">out_cache</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"smodel-index"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="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;">P</span><span class="p">.</span><span class="n" style="color: #333;">smodel_index_for_partition</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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<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">
164
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<td class="diff-line-num new_line old" data-linenumber="181" 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="cpp"> <span class="n" style="color: #333;">out_cache</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"imodel-index"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="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;">P</span><span class="p">.</span><span class="n" style="color: #333;">imodel_index_for_partition</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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<td class="diff-line-num old old_line" data-linenumber="165" 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">
165
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<td class="diff-line-num new_line old" data-linenumber="181" 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="LC165" class="line" lang="cpp"> <span class="n" style="color: #333;">out_cache</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"scale-index"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="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;">P</span><span class="p">.</span><span class="n" style="color: #333;">scale_index_for_partition</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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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 1. filename </span></span>
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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp"> <span class="n" style="color: #333;">out_cache</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"data"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="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;">filenames</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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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"> <span class="n" style="color: #333;">out_screen</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;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">": file = "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">filenames</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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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"> <span class="n" style="color: #333;">partition</span><span class="p">[</span><span class="s" style="color: #d14;">"filename"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filenames</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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166
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="cpp"></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="cpp"> <span class="n" style="color: #333;">json</span> <span class="n" style="color: #333;">partition</span><span class="p">;</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 2. alphabet</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">a_name</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;">get_alphabet</span><span class="p">().</span><span class="n" style="color: #333;">name</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 class="n" style="color: #333;">out_screen</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;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">": alphabet = "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">a_name</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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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp"> <span class="n" style="color: #333;">out_cache</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"alphabet"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="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;">a_name</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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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp"> <span class="n" style="color: #333;">partition</span><span class="p">[</span><span class="s" style="color: #d14;">"alphabet"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a_name</span><span class="p">;</span></span>
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168
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cpp"></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 3. substitution model</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">s_index</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;">smodel_index_for_partition</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="cpp"> <span class="n" style="color: #333;">out_screen</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;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">": subst "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">indent_and_wrap</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">,</span><span class="mi" style="color: #099;">1000</span><span class="p">,</span><span class="n" style="color: #333;">SModels</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s_index</span><span class="p">].</span><span class="n" style="color: #333;">show_main</span><span class="p">(</span><span class="n" style="color: #333;">rules</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">))</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" (S"</span><span class="o" style="font-weight: 600;"><<*</span><span class="n" style="color: #333;">s_index</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="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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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cpp"> <span class="n" style="color: #333;">out_cache</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"smodel-index"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="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;">P</span><span class="p">.</span><span class="n" style="color: #333;">smodel_index_for_partition</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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169
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cpp"> <span class="n" style="color: #333;">partition</span><span class="p">[</span><span class="s" style="color: #d14;">"smodel"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optional_to_json</span><span class="p">(</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">smodel_index_for_partition</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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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 4. indel model</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" 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;">i_index</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;">imodel_index_for_partition</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">))</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp"> <span class="n" style="color: #333;">out_screen</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;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">": indel "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">indent_and_wrap</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">,</span><span class="mi" style="color: #099;">1000</span><span class="p">,</span><span class="n" style="color: #333;">IModels</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i_index</span><span class="p">].</span><span class="n" style="color: #333;">show_main</span><span class="p">(</span><span class="n" style="color: #333;">rules</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">))</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" (I"</span><span class="o" style="font-weight: 600;"><<*</span><span class="n" style="color: #333;">i_index</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="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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<td class="diff-line-num new new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"> <span class="n" style="color: #333;">out_screen</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;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">": indel = none</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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<td class="diff-line-num new new_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp"> <span class="n" style="color: #333;">out_cache</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"imodel-index"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="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;">P</span><span class="p">.</span><span class="n" style="color: #333;">imodel_index_for_partition</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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170
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="cpp"> <span class="n" style="color: #333;">partition</span><span class="p">[</span><span class="s" style="color: #d14;">"imodel"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optional_to_json</span><span class="p">(</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">imodel_index_for_partition</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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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 5. scale model</span></span>
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<td class="diff-line-num new new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">scale_index</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;">scale_index_for_partition</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">out_screen</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;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">": scale "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">indent_and_wrap</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">,</span><span class="mi" style="color: #099;">1000</span><span class="p">,</span><span class="n" style="color: #333;">ScaleModels</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">scale_index</span><span class="p">].</span><span class="n" style="color: #333;">show_main</span><span class="p">(</span><span class="n" style="color: #333;">rules</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">))</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" (Scale"</span><span class="o" style="font-weight: 600;"><<*</span><span class="n" style="color: #333;">scale_index</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="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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<td class="diff-line-num new new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"> <span class="n" style="color: #333;">out_cache</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"scale-index"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="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;">P</span><span class="p">.</span><span class="n" style="color: #333;">scale_index_for_partition</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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171
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp"> <span class="n" style="color: #333;">partition</span><span class="p">[</span><span class="s" style="color: #d14;">"scale"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optional_to_json</span><span class="p">(</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">scale_index_for_partition</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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<td class="diff-line-num old old_line" data-linenumber="172" 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">
172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="cpp"> <span class="n" style="color: #333;">partition</span><span class="p">[</span><span class="s" style="color: #d14;">"filename"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filenames</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="diff-line-num old old_line" data-linenumber="173" 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">
173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="cpp"> <span class="n" style="color: #333;">partition</span><span class="p">[</span><span class="s" style="color: #d14;">"alphabet"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a_name</span><span class="p">;</span></span>
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174
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp"></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp"> <span class="n" style="color: #333;">out_screen</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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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"> <span class="n" style="color: #333;">out_cache</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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175
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cpp"> <span class="n" style="color: #333;">partitions</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">partition</span><span class="p">);</span></span>
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176
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cpp"> <span class="p">}</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="cpp"> <span class="n" style="color: #333;">out_cache</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 old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
178
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp"></span>
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179
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"> <span class="n" style="color: #333;">json</span> <span class="n" style="color: #333;">smodels</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">array</span><span class="p">();</span></span>
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180
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218
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<pre style="margin: 0;"> <span id="LC218" 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="p">.</span><span class="n" style="color: #333;">n_smodels</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="182" style="width: 35px; color: rgba(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="220" style="width: 35px; color: rgba(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">@@ -182,6 +220,9 @@ json log_summary(ostream& out_cache, ostream& out_screen,ostream& out_both,</td>
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<td class="diff-line-num old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
182
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220
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// out_cache<<"subst model"<<i+1<<" = "<<P.SModel(i).name()<<endl<<endl;</span></span>
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<td class="diff-line-num old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
183
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<td class="diff-line-num new_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
221
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;">out_cache</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"subst model"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="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;">SModels</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">show</span><span class="p">(</span><span class="n" style="color: #333;">rules</span><span class="p">)</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</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 old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
184
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222
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;">smodels</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">SModels</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">pretty_model</span><span class="p">());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">e</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;">i</span><span class="p">].</span><span class="n" style="color: #333;">show_extracted</span><span class="p">(</span><span class="n" style="color: #333;">rules</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="185" style="width: 35px; color: rgba(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="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span></span>
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<td class="diff-line-num new new_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"> <span class="n" style="color: #333;">out_screen</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"Substitution model (S"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">") -- priors:"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">e</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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185
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
186
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
187
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<td class="diff-line-num new_line" data-linenumber="228" style="width: 35px; color: rgba(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="LC228" class="line" lang="cpp"> <span class="n" style="color: #333;">json</span> <span class="n" style="color: #333;">imodels</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">array</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="189" style="width: 35px; color: rgba(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="230" style="width: 35px; color: rgba(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">@@ -189,6 +230,9 @@ json log_summary(ostream& out_cache, ostream& out_screen,ostream& out_both,</td>
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<td class="diff-line-num old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
189
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
190
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<td class="diff-line-num new_line" data-linenumber="231" style="width: 35px; color: rgba(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="LC231" class="line" lang="cpp"> <span class="n" style="color: #333;">out_cache</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"indel model"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="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;">IModels</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">show</span><span class="p">(</span><span class="n" style="color: #333;">rules</span><span class="p">)</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</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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191
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp"> <span class="n" style="color: #333;">imodels</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">IModels</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">pretty_model</span><span class="p">());</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IModels</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">show_extracted</span><span class="p">(</span><span class="n" style="color: #333;">rules</span><span class="p">);</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp"> <span class="n" style="color: #333;">out_screen</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"Insertion/deletion model (I"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">") -- priors:"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">e</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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192
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236
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"> <span class="p">}</span></span>
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193
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"></span>
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194
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238
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp"> <span class="n" style="color: #333;">json</span> <span class="n" style="color: #333;">scales</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">array</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="196" style="width: 35px; color: rgba(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="240" style="width: 35px; color: rgba(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">@@ -196,41 +240,9 @@ json log_summary(ostream& out_cache, ostream& out_screen,ostream& out_both,</td>
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196
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240
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"> <span class="p">{</span></span>
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197
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<td class="diff-line-num new_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp"> <span class="n" style="color: #333;">out_cache</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"scale model"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="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;">ScaleModels</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">show</span><span class="p">(</span><span class="n" style="color: #333;">rules</span><span class="p">)</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</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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198
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242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"> <span class="n" style="color: #333;">scales</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ScaleModels</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">pretty_model</span><span class="p">());</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="cpp"> <span class="p">}</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="cpp"></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="cpp"> <span class="n" style="color: #333;">json</span> <span class="n" style="color: #333;">tree</span><span class="p">;</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">t</span><span class="p">().</span><span class="n" style="color: #333;">n_branches</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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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="cpp"> <span class="p">{</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="cpp"> <span class="n" style="color: #333;">out_both</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"T:topology ~ uniform on tree topologies</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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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="cpp"> <span class="n" style="color: #333;">tree</span><span class="p">[</span><span class="s" style="color: #d14;">"topology"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"uniform"</span><span class="p">;</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="cpp"> <span class="p">}</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="cpp"></span>
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208
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<pre style="margin: 0;">-<span id="LC208" 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="p">.</span><span class="n" style="color: #333;">t</span><span class="p">().</span><span class="n" style="color: #333;">n_branches</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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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="cpp"> <span class="n" style="color: #333;">out_both</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"T:lengths "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">branch_length_model</span><span class="p">.</span><span class="n" style="color: #333;">show</span><span class="p">(</span><span class="n" style="color: #333;">rules</span><span class="p">)</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</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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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">tree</span><span class="p">[</span><span class="s" style="color: #d14;">"lengths"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">branch_length_model</span><span class="p">.</span><span class="n" style="color: #333;">show</span><span class="p">(</span><span class="n" style="color: #333;">rules</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="cpp"> <span class="p">}</span></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="cpp"></span>
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214
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<pre style="margin: 0;">-<span id="LC214" 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="p">.</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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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="cpp"> <span class="p">{</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">s_index</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;">smodel_index_for_partition</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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217
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// out_screen<<"#"<<i+1<<": subst ~ "<<P.SModel(s_index).name()<<" ("<<s_index+1<<") ";</span></span>
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218
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="cpp"> <span class="n" style="color: #333;">out_screen</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;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">": alphabet = "</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;">get_data_partition</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">).</span><span class="n" style="color: #333;">get_alphabet</span><span class="p">().</span><span class="n" style="color: #333;">name</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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219
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="cpp"></span>
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220
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="cpp"> <span class="n" style="color: #333;">out_screen</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;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">": subst "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">indent_and_wrap</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">,</span><span class="mi" style="color: #099;">1000</span><span class="p">,</span><span class="n" style="color: #333;">SModels</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s_index</span><span class="p">].</span><span class="n" style="color: #333;">show_pretty</span><span class="p">(</span><span class="n" style="color: #333;">rules</span><span class="p">))</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" (S"</span><span class="o" style="font-weight: 600;"><<*</span><span class="n" style="color: #333;">s_index</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="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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221
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="cpp"></span>
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222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">i_index</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;">imodel_index_for_partition</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="223" 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">
223
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">i_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"= none"</span><span class="p">;</span></span>
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224
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i_index</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="225" 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">
225
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="cpp"> <span class="n" style="color: #333;">i_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indent_and_wrap</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">,</span><span class="mi" style="color: #099;">1000</span><span class="p">,</span><span class="n" style="color: #333;">IModels</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i_index</span><span class="p">].</span><span class="n" style="color: #333;">show_pretty</span><span class="p">(</span><span class="n" style="color: #333;">rules</span><span class="p">));</span></span>
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226
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="cpp"> <span class="n" style="color: #333;">out_screen</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;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">": indel "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">i_name</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i_index</span> <span class="n" style="color: #333;">and</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i_index</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="LC228" class="line" lang="cpp"> <span class="n" style="color: #333;">out_screen</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" (I"</span><span class="o" style="font-weight: 600;"><<*</span><span class="n" style="color: #333;">i_index</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">")"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="cpp"> <span class="n" style="color: #333;">out_screen</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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230
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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="LC231" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">scale_index</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;">scale_index_for_partition</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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232
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="cpp"> <span class="n" style="color: #333;">out_screen</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;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">": scale "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">indent_and_wrap</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">,</span><span class="mi" style="color: #099;">1000</span><span class="p">,</span><span class="n" style="color: #333;">ScaleModels</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">scale_index</span><span class="p">].</span><span class="n" style="color: #333;">show</span><span class="p">(</span><span class="n" style="color: #333;">rules</span><span class="p">))</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" (Scale"</span><span class="o" style="font-weight: 600;"><<*</span><span class="n" style="color: #333;">scale_index</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="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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<pre style="margin: 0;">-<span id="LC233" class="line" lang="cpp"> <span class="n" style="color: #333;">out_screen</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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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ScaleModels</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">show_extracted</span><span class="p">(</span><span class="n" style="color: #333;">rules</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">e</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="LC245" class="line" lang="cpp"> <span class="n" style="color: #333;">out_screen</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"Scale model (Scale"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">") -- priors:"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">e</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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234
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp"> <span class="p">}</span></span>
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235
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247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp"></span>
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236
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cpp"> <span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"partitions"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">partitions</span><span class="p">;</span></span>
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